Index

_

__init__() (navigate.controller.configuration_controller.ConfigurationController method) (navigate.controller.thread_pool.SelfLockThread method) (navigate.controller.thread_pool.SynchronizedThreadPool method) (navigate.controller.thread_pool.ThreadWaitlist method) (navigate.log_files.filters.NonPerfFilter method) (navigate.log_files.filters.PerformanceFilter method) (navigate.model.concurrency.concurrency_tools.CustodyThread method) (navigate.model.concurrency.concurrency_tools.ObjectInSubprocess method) (navigate.model.concurrency.concurrency_tools.ResultThread method) (navigate.model.concurrency.concurrency_tools.SharedNDArray method) (navigate.model.data_sources.bdv_data_source.BigDataViewerDataSource method) (navigate.model.data_sources.data_source.DataSource method) (navigate.model.data_sources.pyramidal_data_source.PyramidalDataSource method) (navigate.model.data_sources.tiff_data_source.TiffDataSource method) (navigate.model.data_sources.zarr_data_source.OMEZarrDataSource method) (navigate.model.device_startup_functions.DummyDeviceConnection method) (navigate.model.device_startup_functions.SerialConnectionFactory method) (navigate.model.devices.APIs.asi.asi_MFC_controller.MFCTwoThousand method) (navigate.model.devices.APIs.asi.asi_MS2000_controller.MS2000Controller method) (navigate.model.devices.APIs.asi.asi_tiger_controller.TigerController method) (navigate.model.devices.APIs.coherent.ObisLaser.ObisLaser method) (navigate.model.devices.APIs.imagineoptics.enums.E_MODAL_T method) (navigate.model.devices.APIs.imagineoptics.enums.E_PUPIL_COVERING_T method) (navigate.model.devices.APIs.imagineoptics.enums.E_PUPIL_DETECTION_T method) (navigate.model.devices.APIs.imagineoptics.enums.E_ZERNIKE_NORM_T method) (navigate.model.devices.APIs.omicron.LuxxLaser.LuxxLaser method) (navigate.model.devices.APIs.sutter.MP285.MP285 method) (navigate.model.devices.camera.base.CameraBase method) (navigate.model.devices.camera.hamamatsu.HamamatsuBase method) (navigate.model.devices.camera.hamamatsu.HamamatsuOrca method) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaFire method) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaFusion method) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaLightning method) (navigate.model.devices.camera.synthetic.SyntheticCamera method) (navigate.model.devices.camera.synthetic.SyntheticCameraController method) (navigate.model.devices.daq.base.DAQBase method) (navigate.model.devices.daq.synthetic.SyntheticDAQ method) (navigate.model.devices.filter_wheel.asi.ASICubeSlider method) (navigate.model.devices.filter_wheel.asi.ASIFilterWheel method) (navigate.model.devices.filter_wheel.base.FilterWheelBase method) (navigate.model.devices.filter_wheel.ludl.LUDLFilterWheel method) (navigate.model.devices.filter_wheel.sutter.SutterFilterWheel method) (navigate.model.devices.filter_wheel.synthetic.SyntheticFilterWheel method) (navigate.model.devices.galvo.base.GalvoBase method) (navigate.model.devices.galvo.synthetic.SyntheticGalvo method) (navigate.model.devices.lasers.base.LaserBase method) (navigate.model.devices.lasers.synthetic.SyntheticLaser method) (navigate.model.devices.mirrors.base.MirrorBase method) (navigate.model.devices.mirrors.imop.ImagineOpticsMirror method) (navigate.model.devices.mirrors.synthetic.SyntheticMirror method) (navigate.model.devices.objectives.Objective method) (navigate.model.devices.remote_focus.base.RemoteFocusBase method) (navigate.model.devices.remote_focus.equipment_solutions.RemoteFocusEquipmentSolutions method) (navigate.model.devices.remote_focus.ni.RemoteFocusNI method) (navigate.model.devices.remote_focus.synthetic.SyntheticRemoteFocus method) (navigate.model.devices.shutter.base.ShutterBase method) (navigate.model.devices.shutter.synthetic.SyntheticShutter method) (navigate.model.devices.stages.asi.ASIStage method) (navigate.model.devices.stages.asi_MSTwoThousand.ASIStage method) (navigate.model.devices.stages.base.StageBase method) (navigate.model.devices.stages.mcl.MCLStage method) (navigate.model.devices.stages.pi.PIStage method) (navigate.model.devices.stages.sutter.SutterStage method) (navigate.model.devices.stages.synthetic.SyntheticStage method) (navigate.model.devices.stages.tl_kcube_inertial.TLKIMStage method) (navigate.model.devices.stages.tl_kcube_steppermotor.TLKSTStage method) (navigate.model.devices.zoom.base.ZoomBase method) (navigate.model.devices.zoom.dynamixel.DynamixelZoom method) (navigate.model.devices.zoom.synthetic.SyntheticZoom method) (navigate.model.features.adaptive_optics.TonyWilson method) (navigate.model.features.auto_tile_scan.CalculateFocusRange method) (navigate.model.features.autofocus.Autofocus method) (navigate.model.features.common_features.ChangeResolution method) (navigate.model.features.common_features.FindTissueSimple2D method) (navigate.model.features.common_features.LoopByCount method) (navigate.model.features.common_features.MoveToNextPositionInMultiPositionTable method) (navigate.model.features.common_features.PrepareNextChannel method) (navigate.model.features.common_features.SetCameraParameters method) (navigate.model.features.common_features.Snap method) (navigate.model.features.common_features.StackPause method) (navigate.model.features.common_features.WaitForExternalTrigger method) (navigate.model.features.common_features.WaitToContinue method) (navigate.model.features.common_features.ZStackAcquisition method) (navigate.model.features.feature_container.Container method) (navigate.model.features.feature_container.DataContainer method) (navigate.model.features.feature_container.DataNode method) (navigate.model.features.feature_container.DummyFeature method) (navigate.model.features.feature_container.SignalContainer method) (navigate.model.features.feature_container.SignalNode method) (navigate.model.features.feature_container.TreeNode method) (navigate.model.features.feature_related_functions.SharedList method) (navigate.model.features.image_writer.ImageWriter method) (navigate.model.features.remove_empty_tiles.DetectTissueInStack method) (navigate.model.features.remove_empty_tiles.DetectTissueInStackAndRecord method) (navigate.model.features.remove_empty_tiles.DetectTissueInStackAndReturn method) (navigate.model.features.remove_empty_tiles.RemoveEmptyPositions method) (navigate.model.features.restful_features.IlastikSegmentation method) (navigate.model.features.volume_search.VolumeSearch method) (navigate.model.metadata_sources.bdv_metadata.BigDataViewerMetadata method) (navigate.model.metadata_sources.metadata.Metadata method) (navigate.model.metadata_sources.metadata.XMLMetadata method) (navigate.model.metadata_sources.ome_tiff_metadata.OMETIFFMetadata method) (navigate.model.metadata_sources.zarr_metadata.OMEZarrMetadata method) (navigate.model.microscope.Microscope method) (navigate.model.model.Model method) (navigate.model.plugins_model.PluginsModel method) (navigate.tools.common_functions.VariableWithLock method) (navigate.tools.decorators.AcquisitionMode method) (navigate.tools.decorators.FeatureList method)

A

acquisition_count (navigate.model.model.Model attribute) AcquisitionMode (class in navigate.tools.decorators) active_microscope (navigate.model.metadata_sources.bdv_metadata.BigDataViewerMetadata attribute) (navigate.model.metadata_sources.metadata.Metadata attribute) (navigate.model.metadata_sources.metadata.XMLMetadata attribute) (navigate.model.metadata_sources.ome_tiff_metadata.OMETIFFMetadata attribute) (navigate.model.metadata_sources.zarr_metadata.OMEZarrMetadata attribute) (navigate.model.model.Model attribute) active_microscope_name (navigate.model.model.Model attribute) add_camera() (navigate.model.devices.daq.synthetic.SyntheticDAQ method) addon_feature (navigate.model.model.Model attribute) addr_mx_goal_position (navigate.model.devices.zoom.dynamixel.DynamixelZoom attribute) addr_mx_moving_speed (navigate.model.devices.zoom.dynamixel.DynamixelZoom attribute) addr_mx_p_gain (navigate.model.devices.zoom.dynamixel.DynamixelZoom attribute) addr_mx_present_position (navigate.model.devices.zoom.dynamixel.DynamixelZoom attribute) addr_mx_torque_enable (navigate.model.devices.zoom.dynamixel.DynamixelZoom attribute) addr_mx_torque_limit (navigate.model.devices.zoom.dynamixel.DynamixelZoom attribute) adjust() (navigate.model.devices.galvo.base.GalvoBase method) (navigate.model.devices.galvo.synthetic.SyntheticGalvo method) (navigate.model.devices.remote_focus.base.RemoteFocusBase method) (navigate.model.devices.remote_focus.equipment_solutions.RemoteFocusEquipmentSolutions method) (navigate.model.devices.remote_focus.ni.RemoteFocusNI method) (navigate.model.devices.remote_focus.synthetic.SyntheticRemoteFocus method) affine_matrix_to_stage_positions() (navigate.model.metadata_sources.bdv_metadata.BigDataViewerMetadata method) affine_rotation() (in module navigate.tools.linear_algebra) affine_shear() (in module navigate.tools.linear_algebra) ALIGNED (navigate.model.concurrency.concurrency_tools.SharedNDArray attribute) all() (navigate.model.concurrency.concurrency_tools.SharedNDArray method) analog_outputs (navigate.model.devices.daq.synthetic.SyntheticDAQ attribute) any() (navigate.model.concurrency.concurrency_tools.SharedNDArray method) append() (navigate.model.features.feature_related_functions.SharedList method) argmax() (navigate.model.concurrency.concurrency_tools.SharedNDArray method) argmin() (navigate.model.concurrency.concurrency_tools.SharedNDArray method) argpartition() (navigate.model.concurrency.concurrency_tools.SharedNDArray method)

argsort() (navigate.model.concurrency.concurrency_tools.SharedNDArray method) asi_axes (navigate.model.devices.stages.asi_MSTwoThousand.ASIStage attribute) ASICubeSlider (class in navigate.model.devices.filter_wheel.asi) ASIFilterWheel (class in navigate.model.devices.filter_wheel.asi) ASIStage (class in navigate.model.devices.stages.asi) (class in navigate.model.devices.stages.asi_MSTwoThousand) ask() (navigate.model.devices.APIs.omicron.LuxxLaser.LuxxLaser method) ask_stage_for_position (navigate.model.microscope.Microscope attribute) ask_to_pause_data_thread (navigate.model.model.Model attribute) assemble_device_config_lists() (navigate.model.microscope.Microscope method) astype() (navigate.model.concurrency.concurrency_tools.SharedNDArray method) auto_redial() (in module navigate.model.device_startup_functions) Autofocus (class in navigate.model.features.autofocus) autofocus (navigate.model.features.auto_tile_scan.CalculateFocusRange attribute) autofocus_frame_queue (navigate.model.features.autofocus.Autofocus attribute) autofocus_pos_queue (navigate.model.features.autofocus.Autofocus attribute) available_channels (navigate.model.microscope.Microscope attribute) axes (navigate.model.devices.stages.asi.ASIStage attribute) (navigate.model.devices.stages.asi_MSTwoThousand.ASIStage attribute) (navigate.model.devices.stages.base.StageBase attribute) (navigate.model.devices.stages.mcl.MCLStage attribute) (navigate.model.devices.stages.pi.PIStage attribute) (navigate.model.devices.stages.sutter.SutterStage attribute) (navigate.model.devices.stages.synthetic.SyntheticStage attribute) (navigate.model.devices.stages.tl_kcube_inertial.TLKIMStage attribute) (navigate.model.devices.stages.tl_kcube_steppermotor.TLKSTStage attribute) axes_mapping (navigate.model.devices.stages.asi.ASIStage attribute) (navigate.model.devices.stages.asi_MSTwoThousand.ASIStage attribute) (navigate.model.devices.stages.base.StageBase attribute) (navigate.model.devices.stages.mcl.MCLStage attribute) (navigate.model.devices.stages.pi.PIStage attribute) (navigate.model.devices.stages.sutter.SutterStage attribute) (navigate.model.devices.stages.synthetic.SyntheticStage attribute) (navigate.model.devices.stages.tl_kcube_inertial.TLKIMStage attribute) (navigate.model.devices.stages.tl_kcube_steppermotor.TLKSTStage attribute)

B

base (navigate.model.concurrency.concurrency_tools.SharedNDArray attribute) baud_rate (navigate.model.devices.APIs.asi.asi_MFC_controller.MFCTwoThousand attribute) (navigate.model.devices.APIs.asi.asi_MS2000_controller.MS2000Controller attribute) (navigate.model.devices.APIs.asi.asi_tiger_controller.TigerController attribute) (navigate.model.devices.remote_focus.equipment_solutions.RemoteFocusEquipmentSolutions attribute) baudrate (in module navigate.model.devices.filter_wheel.ludl) (in module navigate.model.devices.filter_wheel.sutter) bdv_rotate_transform() (navigate.model.metadata_sources.bdv_metadata.BigDataViewerMetadata method) bdv_shear_transform() (navigate.model.metadata_sources.bdv_metadata.BigDataViewerMetadata method) bdv_xml_dict() (navigate.model.metadata_sources.bdv_metadata.BigDataViewerMetadata method) BEHAVED (navigate.model.concurrency.concurrency_tools.SharedNDArray attribute) big_tiff (navigate.model.features.image_writer.ImageWriter attribute) BigDataViewerDataSource (class in navigate.model.data_sources.bdv_data_source) BigDataViewerMetadata (class in navigate.model.metadata_sources.bdv_metadata) binary_detect() (in module navigate.model.analysis.boundary_detect) binning (navigate.model.model.Model attribute) bits (navigate.model.data_sources.bdv_data_source.BigDataViewerDataSource attribute) (navigate.model.data_sources.data_source.DataSource attribute) (navigate.model.data_sources.pyramidal_data_source.PyramidalDataSource attribute) (navigate.model.data_sources.tiff_data_source.TiffDataSource attribute) (navigate.model.data_sources.zarr_data_source.OMEZarrDataSource attribute) board_name (navigate.model.devices.remote_focus.equipment_solutions.RemoteFocusEquipmentSolutions attribute) (navigate.model.devices.remote_focus.ni.RemoteFocusNI attribute)

box() (in module navigate.tools.sdf) build_ASI_Stage_connection() (in module navigate.model.devices.stages.asi) (in module navigate.model.devices.stages.asi_MFCTwoThousand) (in module navigate.model.devices.stages.asi_MSTwoThousand) build_connection() (navigate.model.device_startup_functions.SerialConnectionFactory class method) build_dynamixel_zoom_connection() (in module navigate.model.devices.zoom.dynamixel) build_filter_wheel_connection() (in module navigate.model.devices.filter_wheel.asi) (in module navigate.model.devices.filter_wheel.ludl) (in module navigate.model.devices.filter_wheel.sutter) build_MCLStage_connection() (in module navigate.model.devices.stages.mcl) build_MP285_connection() (in module navigate.model.devices.stages.sutter) build_nested_dict() (in module navigate.config.config) build_PIStage_connection() (in module navigate.model.devices.stages.pi) build_ref_name() (in module navigate.tools.common_functions) build_stage_dict() (navigate.model.devices.zoom.base.ZoomBase method) (navigate.model.devices.zoom.dynamixel.DynamixelZoom method) (navigate.model.devices.zoom.synthetic.SyntheticZoom method) build_TLKIMStage_connection() (in module navigate.model.devices.stages.tl_kcube_inertial) build_TLKSTStage_connection() (in module navigate.model.devices.stages.tl_kcube_steppermotor) byte_size (navigate.model.devices.remote_focus.equipment_solutions.RemoteFocusEquipmentSolutions attribute) byteswap() (navigate.model.concurrency.concurrency_tools.SharedNDArray method)

C

C_CONTIGUOUS (navigate.model.concurrency.concurrency_tools.SharedNDArray attribute) calc_num_tiles() (in module navigate.tools.multipos_table_tools) calculate_all_waveform() (navigate.model.microscope.Microscope method) calculate_all_waveforms() (navigate.model.devices.daq.base.DAQBase method) (navigate.model.devices.daq.synthetic.SyntheticDAQ method) calculate_and_check_disk_space() (navigate.model.features.image_writer.ImageWriter method) calculate_entrance_pupil() (navigate.model.devices.objectives.Objective method) calculate_exposure_sweep_times() (navigate.model.microscope.Microscope method) calculate_light_sheet_exposure_time() (navigate.model.devices.camera.base.CameraBase method) (navigate.model.devices.camera.hamamatsu.HamamatsuBase method) (navigate.model.devices.camera.hamamatsu.HamamatsuOrca method) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaFire method) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaFusion method) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaLightning method) (navigate.model.devices.camera.synthetic.SyntheticCamera method) calculate_readout_time() (navigate.model.devices.camera.hamamatsu.HamamatsuBase method) (navigate.model.devices.camera.hamamatsu.HamamatsuOrca method) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaFire method) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaFusion method) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaLightning method) (navigate.model.devices.camera.synthetic.SyntheticCamera static method) CalculateFocusRange (class in navigate.model.features.auto_tile_scan) camera (navigate.model.devices.daq.synthetic.SyntheticDAQ attribute) (navigate.model.microscope.Microscope attribute) camera_config_dict (navigate.controller.configuration_controller.ConfigurationController property) camera_controller (navigate.model.devices.camera.base.CameraBase attribute) (navigate.model.devices.camera.hamamatsu.HamamatsuBase attribute) (navigate.model.devices.camera.hamamatsu.HamamatsuOrca attribute) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaFire attribute) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaFusion attribute) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaLightning attribute) (navigate.model.devices.camera.synthetic.SyntheticCamera attribute) camera_delay (navigate.model.devices.daq.base.DAQBase attribute) (navigate.model.devices.daq.synthetic.SyntheticDAQ attribute) (navigate.model.devices.galvo.base.GalvoBase attribute) (navigate.model.devices.galvo.synthetic.SyntheticGalvo attribute) (navigate.model.devices.remote_focus.base.RemoteFocusBase attribute) (navigate.model.devices.remote_focus.equipment_solutions.RemoteFocusEquipmentSolutions attribute) (navigate.model.devices.remote_focus.ni.RemoteFocusNI attribute) (navigate.model.devices.remote_focus.synthetic.SyntheticRemoteFocus attribute) camera_exposure() (in module navigate.model.waveforms) camera_exposure_time (navigate.model.devices.camera.synthetic.SyntheticCamera attribute) camera_flip_flags (navigate.controller.configuration_controller.ConfigurationController property) camera_parameters (navigate.model.devices.camera.base.CameraBase attribute) (navigate.model.devices.camera.hamamatsu.HamamatsuBase attribute) (navigate.model.devices.camera.hamamatsu.HamamatsuOrca attribute) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaFire attribute) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaFusion attribute) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaLightning attribute) (navigate.model.devices.camera.synthetic.SyntheticCamera attribute) camera_pixels (navigate.controller.configuration_controller.ConfigurationController property) camera_wait_iterations (navigate.model.model.Model attribute) CameraBase (class in navigate.model.devices.camera.base) CARRAY (navigate.model.concurrency.concurrency_tools.SharedNDArray attribute) center_x (navigate.model.devices.camera.synthetic.SyntheticCamera attribute) center_y (navigate.model.devices.camera.synthetic.SyntheticCamera attribute) central_focus (navigate.model.microscope.Microscope attribute) change_coef (navigate.model.features.adaptive_optics.TonyWilson attribute) change_filter_wheel_speed() (navigate.model.devices.APIs.asi.asi_MFC_controller.MFCTwoThousand method) (navigate.model.devices.APIs.asi.asi_tiger_controller.TigerController method) change_microscope() (navigate.controller.configuration_controller.ConfigurationController method) change_resolution() (navigate.model.model.Model method) ChangeResolution (class in navigate.model.features.common_features) channels (navigate.model.features.common_features.ZStackAcquisition attribute) (navigate.model.microscope.Microscope attribute) channels_info (navigate.controller.configuration_controller.ConfigurationController property) check_if_filter_in_filter_dictionary() (navigate.model.devices.filter_wheel.asi.ASICubeSlider method) (navigate.model.devices.filter_wheel.asi.ASIFilterWheel method) (navigate.model.devices.filter_wheel.base.FilterWheelBase method) (navigate.model.devices.filter_wheel.ludl.LUDLFilterWheel method) (navigate.model.devices.filter_wheel.sutter.SutterFilterWheel method) (navigate.model.devices.filter_wheel.synthetic.SyntheticFilterWheel method) choose() (navigate.model.concurrency.concurrency_tools.SharedNDArray method) cleanup() (navigate.model.features.common_features.ChangeResolution method) (navigate.model.features.common_features.MoveToNextPositionInMultiPositionTable method) (navigate.model.features.common_features.WaitToContinue method) (navigate.model.features.feature_container.Container method) (navigate.model.features.feature_container.DataContainer method) (navigate.model.features.feature_container.SignalContainer method) (navigate.model.features.volume_search.VolumeSearch method) cleanup_data_func() (navigate.model.features.common_features.ZStackAcquisition method) clear() (navigate.controller.thread_pool.SynchronizedThreadPool method) (navigate.model.features.feature_related_functions.SharedList method) clip() (navigate.model.concurrency.concurrency_tools.SharedNDArray method) close() (navigate.model.data_sources.bdv_data_source.BigDataViewerDataSource method) (navigate.model.data_sources.data_source.DataSource method) (navigate.model.data_sources.pyramidal_data_source.PyramidalDataSource method) (navigate.model.data_sources.tiff_data_source.TiffDataSource method) (navigate.model.data_sources.zarr_data_source.OMEZarrDataSource method) (navigate.model.devices.APIs.coherent.ObisLaser.ObisLaser method) (navigate.model.devices.APIs.omicron.LuxxLaser.LuxxLaser method) (navigate.model.devices.APIs.sutter.MP285.MP285 method) (navigate.model.devices.filter_wheel.asi.ASICubeSlider method) (navigate.model.devices.filter_wheel.asi.ASIFilterWheel method) (navigate.model.devices.filter_wheel.ludl.LUDLFilterWheel method) (navigate.model.devices.filter_wheel.sutter.SutterFilterWheel method) (navigate.model.devices.filter_wheel.synthetic.SyntheticFilterWheel method) (navigate.model.devices.lasers.base.LaserBase method) (navigate.model.devices.lasers.synthetic.SyntheticLaser method) (navigate.model.devices.stages.asi.ASIStage method) (navigate.model.devices.stages.asi_MSTwoThousand.ASIStage method) (navigate.model.devices.stages.base.StageBase method) (navigate.model.devices.stages.mcl.MCLStage method) (navigate.model.devices.stages.pi.PIStage method) (navigate.model.devices.stages.sutter.SutterStage method) (navigate.model.devices.stages.synthetic.SyntheticStage method) (navigate.model.devices.stages.tl_kcube_inertial.TLKIMStage method) (navigate.model.devices.stages.tl_kcube_steppermotor.TLKSTStage method) (navigate.model.features.image_writer.ImageWriter method) close_camera() (navigate.model.devices.camera.base.CameraBase method) (navigate.model.devices.camera.hamamatsu.HamamatsuBase method) (navigate.model.devices.camera.hamamatsu.HamamatsuOrca method) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaFire method) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaFusion method) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaLightning method) (navigate.model.devices.camera.synthetic.SyntheticCamera method) close_image_series() (navigate.model.devices.camera.hamamatsu.HamamatsuBase method) (navigate.model.devices.camera.hamamatsu.HamamatsuOrca method) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaFire method) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaFusion method) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaLightning method) (navigate.model.devices.camera.synthetic.SyntheticCamera method)

close_shutter() (navigate.model.devices.shutter.base.ShutterBase method) (navigate.model.devices.shutter.synthetic.SyntheticShutter method) close_tasks() (navigate.model.devices.daq.synthetic.SyntheticDAQ method) coarse_step_size (navigate.model.features.autofocus.Autofocus attribute) coarse_steps (navigate.model.features.autofocus.Autofocus attribute) coef_amp (navigate.model.features.adaptive_optics.TonyWilson attribute) com_port (navigate.model.devices.APIs.asi.asi_MFC_controller.MFCTwoThousand attribute) (navigate.model.devices.APIs.asi.asi_MS2000_controller.MS2000Controller attribute) (navigate.model.devices.APIs.asi.asi_tiger_controller.TigerController attribute) combine_funcs() (in module navigate.tools.common_functions) commands (navigate.model.microscope.Microscope attribute) commands_buffer (navigate.model.devices.APIs.sutter.MP285.MP285 attribute) commands_num (navigate.model.devices.APIs.sutter.MP285.MP285 attribute) comport (in module navigate.model.devices.filter_wheel.ludl) (in module navigate.model.devices.filter_wheel.sutter) (navigate.model.devices.remote_focus.equipment_solutions.RemoteFocusEquipmentSolutions attribute) compress() (navigate.model.concurrency.concurrency_tools.SharedNDArray method) compute_flatfield_map() (in module navigate.model.analysis.camera) compute_noise_sigma() (in module navigate.model.analysis.camera) compute_scmos_offset_and_variance_map() (in module navigate.model.analysis.camera) compute_signal_to_noise() (in module navigate.model.analysis.camera) compute_tiles_from_bounding_box() (in module navigate.tools.multipos_table_tools) config_table (navigate.model.features.autofocus.Autofocus attribute) (navigate.model.features.common_features.ChangeResolution attribute) (navigate.model.features.common_features.FindTissueSimple2D attribute) (navigate.model.features.common_features.LoopByCount attribute) (navigate.model.features.common_features.MoveToNextPositionInMultiPositionTable attribute) (navigate.model.features.common_features.PrepareNextChannel attribute) (navigate.model.features.common_features.SetCameraParameters attribute) (navigate.model.features.common_features.Snap attribute) (navigate.model.features.common_features.WaitToContinue attribute) (navigate.model.features.common_features.ZStackAcquisition attribute) (navigate.model.features.image_writer.ImageWriter attribute) (navigate.model.features.restful_features.IlastikSegmentation attribute) (navigate.model.features.volume_search.VolumeSearch attribute) configuration (navigate.controller.configuration_controller.ConfigurationController attribute) (navigate.model.devices.APIs.coherent.ObisLaser.ObisLaser attribute) (navigate.model.devices.APIs.omicron.LuxxLaser.LuxxLaser attribute) (navigate.model.devices.camera.base.CameraBase attribute) (navigate.model.devices.camera.hamamatsu.HamamatsuBase attribute) (navigate.model.devices.camera.hamamatsu.HamamatsuOrca attribute) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaFire attribute) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaFusion attribute) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaLightning attribute) (navigate.model.devices.camera.synthetic.SyntheticCamera attribute) (navigate.model.devices.daq.base.DAQBase attribute) (navigate.model.devices.daq.synthetic.SyntheticDAQ attribute) (navigate.model.devices.galvo.base.GalvoBase attribute) (navigate.model.devices.galvo.synthetic.SyntheticGalvo attribute) (navigate.model.devices.lasers.base.LaserBase attribute) (navigate.model.devices.lasers.synthetic.SyntheticLaser attribute) (navigate.model.devices.mirrors.base.MirrorBase attribute) (navigate.model.devices.mirrors.imop.ImagineOpticsMirror attribute) (navigate.model.devices.mirrors.synthetic.SyntheticMirror attribute) (navigate.model.devices.remote_focus.base.RemoteFocusBase attribute) (navigate.model.devices.remote_focus.equipment_solutions.RemoteFocusEquipmentSolutions attribute) (navigate.model.devices.remote_focus.ni.RemoteFocusNI attribute) (navigate.model.devices.remote_focus.synthetic.SyntheticRemoteFocus attribute) (navigate.model.devices.shutter.base.ShutterBase attribute) (navigate.model.devices.shutter.synthetic.SyntheticShutter attribute) (navigate.model.devices.zoom.base.ZoomBase attribute) (navigate.model.devices.zoom.dynamixel.DynamixelZoom attribute) (navigate.model.devices.zoom.synthetic.SyntheticZoom attribute) (navigate.model.metadata_sources.bdv_metadata.BigDataViewerMetadata property) (navigate.model.metadata_sources.metadata.Metadata property) (navigate.model.metadata_sources.metadata.XMLMetadata property) (navigate.model.metadata_sources.ome_tiff_metadata.OMETIFFMetadata property) (navigate.model.metadata_sources.zarr_metadata.OMEZarrMetadata property) (navigate.model.microscope.Microscope attribute) (navigate.model.model.Model attribute) ConfigurationController (class in navigate.controller.configuration_controller) conj() (navigate.model.concurrency.concurrency_tools.SharedNDArray method) conjugate() (navigate.model.concurrency.concurrency_tools.SharedNDArray method) connect_to_serial() (navigate.model.devices.APIs.asi.asi_MFC_controller.MFCTwoThousand method) (navigate.model.devices.APIs.asi.asi_MS2000_controller.MS2000Controller method) (navigate.model.devices.APIs.asi.asi_tiger_controller.TigerController method) (navigate.model.devices.APIs.sutter.MP285.MP285 method) Container (class in navigate.model.features.feature_container) convert_feature_list_to_str() (in module navigate.model.features.feature_related_functions) convert_microns_to_microsteps() (navigate.model.devices.APIs.sutter.MP285.MP285 static method) convert_microsteps_to_microns() (navigate.model.devices.APIs.sutter.MP285.MP285 static method) convert_str_to_feature_list() (in module navigate.model.features.feature_related_functions) copy() (navigate.model.concurrency.concurrency_tools.SharedNDArray method) (navigate.model.features.feature_related_functions.SharedList method) copy_proxy_object() (in module navigate.tools.common_functions) count() (navigate.model.features.feature_related_functions.SharedList method) create_arrow_image() (in module navigate.tools.image) create_camera_task() (navigate.model.devices.daq.synthetic.SyntheticDAQ method) create_galvo_remote_focus_tasks() (navigate.model.devices.daq.synthetic.SyntheticDAQ method) create_master_trigger_task() (navigate.model.devices.daq.synthetic.SyntheticDAQ method) create_mock_dxl_device() (in module navigate.model.devices.APIs.dynamixel.dynamixel_functions) create_parser() (in module navigate.tools.main_functions) create_pipe() (navigate.model.model.Model method) create_save_path() (in module navigate.tools.file_functions) createThread() (navigate.controller.thread_pool.SynchronizedThreadPool method) ctypes (navigate.model.concurrency.concurrency_tools.SharedNDArray attribute) cumprod() (navigate.model.concurrency.concurrency_tools.SharedNDArray method) cumsum() (navigate.model.concurrency.concurrency_tools.SharedNDArray method) curr_node (navigate.model.features.feature_container.Container attribute) (navigate.model.features.feature_container.DataContainer attribute) (navigate.model.features.feature_container.SignalContainer attribute) curr_z_index (navigate.model.features.volume_search.VolumeSearch attribute) current_channel (navigate.model.microscope.Microscope attribute) current_exposure_time (navigate.model.model.Model attribute) current_focus_position (navigate.model.features.common_features.ZStackAcquisition attribute) current_frame_idx (navigate.model.devices.camera.synthetic.SyntheticCamera attribute) current_idx (navigate.model.features.common_features.MoveToNextPositionInMultiPositionTable attribute) current_laser_index (navigate.model.microscope.Microscope attribute) current_position_idx (navigate.model.features.common_features.ZStackAcquisition attribute) current_tif_id (navigate.model.devices.camera.synthetic.SyntheticCamera attribute) current_time_point (navigate.model.features.image_writer.ImageWriter attribute) current_z_position (navigate.model.features.common_features.ZStackAcquisition attribute) CustodyThread (class in navigate.model.concurrency.concurrency_tools)

D

daemon (navigate.controller.thread_pool.SelfLockThread property) (navigate.model.concurrency.concurrency_tools.CustodyThread property) (navigate.model.concurrency.concurrency_tools.ResultThread property) daq (navigate.model.devices.remote_focus.equipment_solutions.RemoteFocusEquipmentSolutions attribute) (navigate.model.devices.remote_focus.ni.RemoteFocusNI attribute) (navigate.model.microscope.Microscope attribute) daq_parameters (navigate.model.devices.daq.base.DAQBase attribute) (navigate.model.devices.daq.synthetic.SyntheticDAQ attribute) daq_sample_rate (navigate.controller.configuration_controller.ConfigurationController property) DAQBase (class in navigate.model.devices.daq.base) data (navigate.model.concurrency.concurrency_tools.SharedNDArray attribute) (navigate.model.data_sources.bdv_data_source.BigDataViewerDataSource property) (navigate.model.data_sources.data_source.DataSource property) (navigate.model.data_sources.pyramidal_data_source.PyramidalDataSource property) (navigate.model.data_sources.tiff_data_source.TiffDataSource property) (navigate.model.data_sources.zarr_data_source.OMEZarrDataSource property) data_buffer (navigate.model.devices.camera.synthetic.SyntheticCamera attribute) (navigate.model.features.image_writer.ImageWriter attribute) (navigate.model.microscope.Microscope attribute) (navigate.model.model.Model attribute) data_buffer_positions (navigate.model.model.Model attribute) data_buffer_saving_flags (navigate.model.model.Model attribute) data_frames (navigate.model.features.common_features.LoopByCount attribute) data_func() (navigate.model.features.common_features.FindTissueSimple2D method) (navigate.model.features.common_features.LoopByCount method) (navigate.model.features.common_features.Snap method) (navigate.model.features.common_features.WaitToContinue method) (navigate.model.features.restful_features.IlastikSegmentation method) (navigate.model.features.volume_search.VolumeSearch method) data_source (navigate.model.features.image_writer.ImageWriter attribute) data_thread (navigate.model.model.Model attribute) DataContainer (class in navigate.model.features.feature_container) DataNode (class in navigate.model.features.feature_container) DataSource (class in navigate.model.data_sources.data_source) dc (navigate.model.data_sources.bdv_data_source.BigDataViewerDataSource attribute) (navigate.model.data_sources.data_source.DataSource attribute) (navigate.model.data_sources.pyramidal_data_source.PyramidalDataSource attribute) (navigate.model.data_sources.tiff_data_source.TiffDataSource attribute) (navigate.model.data_sources.zarr_data_source.OMEZarrDataSource attribute) (navigate.model.metadata_sources.bdv_metadata.BigDataViewerMetadata attribute) (navigate.model.metadata_sources.metadata.Metadata attribute) (navigate.model.metadata_sources.metadata.XMLMetadata attribute) (navigate.model.metadata_sources.ome_tiff_metadata.OMETIFFMetadata attribute) (navigate.model.metadata_sources.zarr_metadata.OMEZarrMetadata attribute) dc_value() (in module navigate.model.waveforms) debug (navigate.model.devices.remote_focus.equipment_solutions.RemoteFocusEquipmentSolutions attribute) (navigate.model.features.volume_search.VolumeSearch attribute) default_axes_sequence (navigate.model.devices.APIs.asi.asi_MFC_controller.MFCTwoThousand attribute) (navigate.model.devices.APIs.asi.asi_MS2000_controller.MS2000Controller attribute) (navigate.model.devices.APIs.asi.asi_tiger_controller.TigerController attribute) default_speed (navigate.model.devices.stages.synthetic.SyntheticStage attribute) defocus (navigate.model.features.common_features.ZStackAcquisition attribute) delay_matrix (navigate.model.devices.filter_wheel.sutter.SutterFilterWheel attribute) delete_folder() (in module navigate.tools.file_functions) destroy_virtual_microscope() (navigate.model.model.Model method) detect_func (navigate.model.features.remove_empty_tiles.DetectTissueInStack attribute) (navigate.model.features.remove_empty_tiles.DetectTissueInStackAndRecord attribute) (navigate.model.features.remove_empty_tiles.DetectTissueInStackAndReturn attribute) detect_tissue() (in module navigate.model.features.remove_empty_tiles) detect_tissue2() (in module navigate.model.features.remove_empty_tiles) DetectTissueInStack (class in navigate.model.features.remove_empty_tiles) DetectTissueInStackAndRecord (class in navigate.model.features.remove_empty_tiles) DetectTissueInStackAndReturn (class in navigate.model.features.remove_empty_tiles) device (navigate.model.features.autofocus.Autofocus attribute) device_axes (navigate.model.devices.stages.sutter.SutterStage attribute) device_config (navigate.model.devices.APIs.coherent.ObisLaser.ObisLaser attribute) (navigate.model.devices.APIs.omicron.LuxxLaser.LuxxLaser attribute) (navigate.model.devices.filter_wheel.asi.ASICubeSlider attribute) (navigate.model.devices.filter_wheel.asi.ASIFilterWheel attribute) (navigate.model.devices.filter_wheel.base.FilterWheelBase attribute) (navigate.model.devices.filter_wheel.ludl.LUDLFilterWheel attribute) (navigate.model.devices.filter_wheel.sutter.SutterFilterWheel attribute) (navigate.model.devices.filter_wheel.synthetic.SyntheticFilterWheel attribute) (navigate.model.devices.galvo.base.GalvoBase attribute) (navigate.model.devices.galvo.synthetic.SyntheticGalvo attribute) (navigate.model.devices.lasers.base.LaserBase attribute) (navigate.model.devices.lasers.synthetic.SyntheticLaser attribute) (navigate.model.devices.remote_focus.base.RemoteFocusBase attribute) (navigate.model.devices.remote_focus.equipment_solutions.RemoteFocusEquipmentSolutions attribute) (navigate.model.devices.remote_focus.ni.RemoteFocusNI attribute) (navigate.model.devices.remote_focus.synthetic.SyntheticRemoteFocus attribute) device_connection (navigate.model.devices.APIs.coherent.ObisLaser.ObisLaser attribute) (navigate.model.devices.APIs.omicron.LuxxLaser.LuxxLaser attribute) (navigate.model.devices.camera.hamamatsu.HamamatsuBase attribute) (navigate.model.devices.camera.hamamatsu.HamamatsuOrca attribute) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaFire attribute) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaFusion attribute) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaLightning attribute) (navigate.model.devices.camera.synthetic.SyntheticCamera attribute) (navigate.model.devices.filter_wheel.asi.ASICubeSlider attribute) (navigate.model.devices.filter_wheel.asi.ASIFilterWheel attribute) (navigate.model.devices.filter_wheel.base.FilterWheelBase attribute) (navigate.model.devices.filter_wheel.ludl.LUDLFilterWheel attribute) (navigate.model.devices.filter_wheel.sutter.SutterFilterWheel attribute) (navigate.model.devices.filter_wheel.synthetic.SyntheticFilterWheel attribute) (navigate.model.devices.galvo.base.GalvoBase attribute) (navigate.model.devices.galvo.synthetic.SyntheticGalvo attribute) (navigate.model.devices.lasers.base.LaserBase attribute) (navigate.model.devices.lasers.synthetic.SyntheticLaser attribute) (navigate.model.devices.remote_focus.base.RemoteFocusBase attribute) (navigate.model.devices.remote_focus.equipment_solutions.RemoteFocusEquipmentSolutions attribute) (navigate.model.devices.remote_focus.ni.RemoteFocusNI attribute) (navigate.model.devices.remote_focus.synthetic.SyntheticRemoteFocus attribute) (navigate.model.devices.shutter.base.ShutterBase attribute) (navigate.model.devices.shutter.synthetic.SyntheticShutter attribute) (navigate.model.devices.stages.asi.ASIStage attribute) (navigate.model.devices.stages.asi_MSTwoThousand.ASIStage attribute) (navigate.model.devices.stages.base.StageBase attribute) (navigate.model.devices.stages.mcl.MCLStage attribute) (navigate.model.devices.stages.pi.PIStage attribute) (navigate.model.devices.stages.sutter.SutterStage attribute) (navigate.model.devices.stages.synthetic.SyntheticStage attribute) (navigate.model.devices.stages.tl_kcube_inertial.TLKIMStage attribute) (navigate.model.devices.stages.tl_kcube_steppermotor.TLKSTStage attribute)

device_not_found() (in module navigate.model.device_startup_functions) device_ref (navigate.model.features.autofocus.Autofocus attribute) device_related (navigate.model.features.feature_container.DataNode attribute) (navigate.model.features.feature_container.SignalNode attribute) (navigate.model.features.feature_container.TreeNode attribute) device_unit_scale (navigate.model.devices.stages.tl_kcube_steppermotor.TLKSTStage attribute) devices_dict (navigate.model.plugins_model.PluginsModel attribute) diagonal() (navigate.model.concurrency.concurrency_tools.SharedNDArray method) dichroic (navigate.model.devices.filter_wheel.asi.ASICubeSlider attribute) dichroic_id (navigate.model.devices.filter_wheel.asi.ASICubeSlider attribute) dichroic_position (navigate.model.devices.filter_wheel.asi.ASICubeSlider attribute) dict_to_xml() (in module navigate.tools.xml_tools) direction (navigate.model.features.volume_search.VolumeSearch attribute) disconnect_from_serial() (navigate.model.devices.APIs.asi.asi_MFC_controller.MFCTwoThousand method) (navigate.model.devices.APIs.asi.asi_MS2000_controller.MS2000Controller method) (navigate.model.devices.APIs.asi.asi_tiger_controller.TigerController method) (navigate.model.devices.APIs.sutter.MP285.MP285 method) display_modes() (navigate.model.devices.mirrors.imop.ImagineOpticsMirror method) done_all (navigate.model.features.adaptive_optics.TonyWilson attribute) done_itr (navigate.model.features.adaptive_optics.TonyWilson attribute) draw_box() (in module navigate.model.features.volume_search) dt (navigate.model.data_sources.bdv_data_source.BigDataViewerDataSource attribute) (navigate.model.data_sources.data_source.DataSource attribute) (navigate.model.data_sources.pyramidal_data_source.PyramidalDataSource attribute) (navigate.model.data_sources.tiff_data_source.TiffDataSource attribute) (navigate.model.data_sources.zarr_data_source.OMEZarrDataSource attribute) (navigate.model.metadata_sources.bdv_metadata.BigDataViewerMetadata attribute) (navigate.model.metadata_sources.metadata.Metadata attribute) (navigate.model.metadata_sources.metadata.XMLMetadata attribute) (navigate.model.metadata_sources.ome_tiff_metadata.OMETIFFMetadata attribute) (navigate.model.metadata_sources.zarr_metadata.OMEZarrMetadata attribute) dtype (navigate.model.concurrency.concurrency_tools.SharedNDArray attribute) dummy_func() (in module navigate.model.features.feature_container) dummy_True() (in module navigate.model.features.feature_container) DummyDeviceConnection (class in navigate.model.device_startup_functions) DummyFeature (class in navigate.model.features.feature_container) dump() (navigate.model.concurrency.concurrency_tools.SharedNDArray method) dumps() (navigate.model.concurrency.concurrency_tools.SharedNDArray method) dx (navigate.model.data_sources.bdv_data_source.BigDataViewerDataSource attribute) (navigate.model.data_sources.data_source.DataSource attribute) (navigate.model.data_sources.pyramidal_data_source.PyramidalDataSource attribute) (navigate.model.data_sources.tiff_data_source.TiffDataSource attribute) (navigate.model.data_sources.zarr_data_source.OMEZarrDataSource attribute) (navigate.model.metadata_sources.bdv_metadata.BigDataViewerMetadata attribute) (navigate.model.metadata_sources.metadata.Metadata attribute) (navigate.model.metadata_sources.metadata.XMLMetadata attribute) (navigate.model.metadata_sources.ome_tiff_metadata.OMETIFFMetadata attribute) (navigate.model.metadata_sources.zarr_metadata.OMEZarrMetadata attribute) dy (navigate.model.data_sources.bdv_data_source.BigDataViewerDataSource attribute) (navigate.model.data_sources.data_source.DataSource attribute) (navigate.model.data_sources.pyramidal_data_source.PyramidalDataSource attribute) (navigate.model.data_sources.tiff_data_source.TiffDataSource attribute) (navigate.model.data_sources.zarr_data_source.OMEZarrDataSource attribute) (navigate.model.metadata_sources.bdv_metadata.BigDataViewerMetadata attribute) (navigate.model.metadata_sources.metadata.Metadata attribute) (navigate.model.metadata_sources.metadata.XMLMetadata attribute) (navigate.model.metadata_sources.ome_tiff_metadata.OMETIFFMetadata attribute) (navigate.model.metadata_sources.zarr_metadata.OMEZarrMetadata attribute) dynamixel (navigate.model.devices.zoom.dynamixel.DynamixelZoom attribute) DynamixelZoom (class in navigate.model.devices.zoom.dynamixel) dz (navigate.model.data_sources.bdv_data_source.BigDataViewerDataSource attribute) (navigate.model.data_sources.data_source.DataSource attribute) (navigate.model.data_sources.pyramidal_data_source.PyramidalDataSource attribute) (navigate.model.data_sources.tiff_data_source.TiffDataSource attribute) (navigate.model.data_sources.zarr_data_source.OMEZarrDataSource attribute) (navigate.model.metadata_sources.bdv_metadata.BigDataViewerMetadata attribute) (navigate.model.metadata_sources.metadata.Metadata attribute) (navigate.model.metadata_sources.metadata.XMLMetadata attribute) (navigate.model.metadata_sources.ome_tiff_metadata.OMETIFFMetadata attribute) (navigate.model.metadata_sources.zarr_metadata.OMEZarrMetadata attribute)

E

E_MODAL_T (class in navigate.model.devices.APIs.imagineoptics.enums) E_PUPIL_COVERING_T (class in navigate.model.devices.APIs.imagineoptics.enums) E_PUPIL_DETECTION_T (class in navigate.model.devices.APIs.imagineoptics.enums) E_ZERNIKE_NORM_T (class in navigate.model.devices.APIs.imagineoptics.enums) eliminate_old_log_files() (in module navigate.log_files.log_functions) ellipsoid() (in module navigate.tools.sdf) enable_microscope() (navigate.model.devices.daq.base.DAQBase method) (navigate.model.devices.daq.synthetic.SyntheticDAQ method) end_acquisition() (navigate.model.microscope.Microscope method) (navigate.model.model.Model method) end_data_func() (navigate.model.features.common_features.ZStackAcquisition method) (navigate.model.features.volume_search.VolumeSearch method) end_flag (navigate.model.features.feature_container.Container attribute) (navigate.model.features.feature_container.DataContainer attribute) (navigate.model.features.feature_container.SignalContainer attribute) (navigate.model.features.volume_search.VolumeSearch attribute) end_func_data() (navigate.model.features.adaptive_optics.TonyWilson method) (navigate.model.features.auto_tile_scan.CalculateFocusRange method) (navigate.model.features.autofocus.Autofocus method) (navigate.model.features.remove_empty_tiles.DetectTissueInStack method) (navigate.model.features.remove_empty_tiles.DetectTissueInStackAndRecord method) (navigate.model.features.remove_empty_tiles.DetectTissueInStackAndReturn method)

end_func_signal() (navigate.model.features.adaptive_optics.TonyWilson method) (navigate.model.features.auto_tile_scan.CalculateFocusRange method) (navigate.model.features.autofocus.Autofocus method) (navigate.model.features.remove_empty_tiles.DetectTissueInStack method) (navigate.model.features.remove_empty_tiles.DetectTissueInStackAndRecord method) (navigate.model.features.remove_empty_tiles.DetectTissueInStackAndReturn method) end_of_line (navigate.model.devices.APIs.coherent.ObisLaser.ObisLaser attribute) ensure_iter() (in module navigate.tools.slicing) ensure_slice() (in module navigate.tools.slicing) evaluate_parser_input_arguments() (in module navigate.tools.main_functions) event_queue (navigate.model.model.Model attribute) exposure_times (navigate.model.devices.daq.base.DAQBase attribute) (navigate.model.devices.daq.synthetic.SyntheticDAQ attribute) extend() (navigate.model.features.feature_related_functions.SharedList method)

F

F_CONTIGUOUS (navigate.model.concurrency.concurrency_tools.SharedNDArray attribute) f_frame_id (navigate.model.features.autofocus.Autofocus attribute) f_offset (navigate.model.features.volume_search.VolumeSearch attribute) f_pos (navigate.model.features.autofocus.Autofocus attribute) (navigate.model.features.volume_search.VolumeSearch attribute) f_position (navigate.model.model.Model attribute) f_step_size (navigate.model.features.volume_search.VolumeSearch attribute) FancyThread (in module navigate.model.concurrency.concurrency_tools) FARRAY (navigate.model.concurrency.concurrency_tools.SharedNDArray attribute) fast_normalized_dct_shannon_entropy() (in module navigate.model.analysis.image_contrast) feature_list (navigate.model.model.Model attribute) feature_lists_path (navigate.model.plugins_model.PluginsModel attribute) FeatureList (class in navigate.tools.decorators) file_name (navigate.model.data_sources.bdv_data_source.BigDataViewerDataSource attribute) (navigate.model.data_sources.data_source.DataSource attribute) (navigate.model.data_sources.pyramidal_data_source.PyramidalDataSource attribute) (navigate.model.data_sources.tiff_data_source.TiffDataSource attribute) (navigate.model.data_sources.zarr_data_source.OMEZarrDataSource attribute) file_type (navigate.model.features.image_writer.ImageWriter attribute) fill() (navigate.model.concurrency.concurrency_tools.SharedNDArray method) filter() (navigate.log_files.filters.NonPerfFilter method) (navigate.log_files.filters.PerformanceFilter method) filter_change_delay() (navigate.model.devices.filter_wheel.asi.ASICubeSlider method) (navigate.model.devices.filter_wheel.asi.ASIFilterWheel method) (navigate.model.devices.filter_wheel.sutter.SutterFilterWheel method) (navigate.model.devices.filter_wheel.synthetic.SyntheticFilterWheel method) filter_dictionary (navigate.model.devices.filter_wheel.asi.ASICubeSlider attribute) (navigate.model.devices.filter_wheel.asi.ASIFilterWheel attribute) (navigate.model.devices.filter_wheel.base.FilterWheelBase attribute) (navigate.model.devices.filter_wheel.ludl.LUDLFilterWheel attribute) (navigate.model.devices.filter_wheel.sutter.SutterFilterWheel attribute) (navigate.model.devices.filter_wheel.synthetic.SyntheticFilterWheel attribute)

filter_wheel (navigate.model.devices.filter_wheel.asi.ASIFilterWheel attribute) (navigate.model.microscope.Microscope attribute) filter_wheel_names (navigate.controller.configuration_controller.ConfigurationController property) filter_wheel_number (navigate.model.devices.filter_wheel.asi.ASICubeSlider attribute) (navigate.model.devices.filter_wheel.asi.ASIFilterWheel attribute) (navigate.model.devices.filter_wheel.base.FilterWheelBase attribute) (navigate.model.devices.filter_wheel.ludl.LUDLFilterWheel attribute) (navigate.model.devices.filter_wheel.sutter.SutterFilterWheel attribute) (navigate.model.devices.filter_wheel.synthetic.SyntheticFilterWheel attribute) filter_wheel_position (navigate.model.devices.filter_wheel.asi.ASIFilterWheel attribute) filter_wheel_setting_dict (navigate.controller.configuration_controller.ConfigurationController property) FilterWheelBase (class in navigate.model.devices.filter_wheel.base) find_filename() (in module navigate.log_files.log_functions) find_tissue_boundary_2d() (in module navigate.model.analysis.boundary_detect) FindTissueSimple2D (class in navigate.model.features.common_features) fine_pos_offset (navigate.model.features.autofocus.Autofocus attribute) fine_step_size (navigate.model.features.autofocus.Autofocus attribute) first_boundary (navigate.model.features.volume_search.VolumeSearch attribute) first_enter_node (navigate.model.features.common_features.WaitToContinue attribute) flags (navigate.model.concurrency.concurrency_tools.SharedNDArray attribute) flat (navigate.model.concurrency.concurrency_tools.SharedNDArray attribute) flat() (navigate.model.devices.mirrors.imop.ImagineOpticsMirror method) (navigate.model.devices.mirrors.synthetic.SyntheticMirror method) flatten() (navigate.model.concurrency.concurrency_tools.SharedNDArray method) FNC (navigate.model.concurrency.concurrency_tools.SharedNDArray attribute) focus_pos (navigate.model.features.autofocus.Autofocus attribute) (navigate.model.model.Model attribute) focus_step_size (navigate.model.features.common_features.ZStackAcquisition attribute) FORC (navigate.model.concurrency.concurrency_tools.SharedNDArray attribute) fourier_annulus() (in module navigate.model.features.adaptive_optics) frame_id (navigate.model.model.Model attribute) frame_num (navigate.model.features.autofocus.Autofocus attribute) function_timer() (in module navigate.tools.decorators)

G

galvo (navigate.model.microscope.Microscope attribute) galvo_id (navigate.model.devices.galvo.synthetic.SyntheticGalvo attribute) galvo_max_voltage (navigate.model.devices.galvo.base.GalvoBase attribute) (navigate.model.devices.galvo.synthetic.SyntheticGalvo attribute) galvo_min_voltage (navigate.model.devices.galvo.base.GalvoBase attribute) (navigate.model.devices.galvo.synthetic.SyntheticGalvo attribute) galvo_name (navigate.model.devices.galvo.base.GalvoBase attribute) (navigate.model.devices.galvo.synthetic.SyntheticGalvo attribute) galvo_num (navigate.controller.configuration_controller.ConfigurationController attribute) galvo_parameter_dict (navigate.controller.configuration_controller.ConfigurationController property) galvo_waveform (navigate.model.devices.galvo.base.GalvoBase attribute) (navigate.model.devices.galvo.synthetic.SyntheticGalvo attribute) GalvoBase (class in navigate.model.devices.galvo.base) gauss() (in module navigate.model.features.adaptive_optics) generate_image_name() (navigate.model.data_sources.tiff_data_source.TiffDataSource method) (navigate.model.features.image_writer.ImageWriter method) generate_new_frame() (navigate.model.devices.camera.synthetic.SyntheticCamera method) get_abs_position() (navigate.model.devices.stages.asi.ASIStage method) (navigate.model.devices.stages.asi_MSTwoThousand.ASIStage method) (navigate.model.devices.stages.base.StageBase method) (navigate.model.devices.stages.mcl.MCLStage method) (navigate.model.devices.stages.pi.PIStage method) (navigate.model.devices.stages.sutter.SutterStage method) (navigate.model.devices.stages.synthetic.SyntheticStage method) (navigate.model.devices.stages.tl_kcube_inertial.TLKIMStage method) (navigate.model.devices.stages.tl_kcube_steppermotor.TLKSTStage method) get_active_microscope() (navigate.model.model.Model method) get_affine_parameters() (navigate.model.metadata_sources.bdv_metadata.BigDataViewerMetadata method) get_autofocus_frame_num() (navigate.model.features.autofocus.Autofocus method) get_autostart() (navigate.model.devices.APIs.omicron.LuxxLaser.LuxxLaser method) get_available_channels() (navigate.model.microscope.Microscope method) get_axis_position() (navigate.model.devices.APIs.asi.asi_MFC_controller.MFCTwoThousand method) (navigate.model.devices.APIs.asi.asi_MS2000_controller.MS2000Controller method) (navigate.model.devices.APIs.asi.asi_tiger_controller.TigerController method) (navigate.model.devices.stages.asi.ASIStage method) (navigate.model.devices.stages.asi_MSTwoThousand.ASIStage method) (navigate.model.devices.stages.synthetic.SyntheticStage method) get_axis_position_um() (navigate.model.devices.APIs.asi.asi_MFC_controller.MFCTwoThousand method) (navigate.model.devices.APIs.asi.asi_MS2000_controller.MS2000Controller method) (navigate.model.devices.APIs.asi.asi_tiger_controller.TigerController method) get_camera_line_interval_and_exposure_time() (navigate.model.model.Model method) get_configuration_paths() (in module navigate.config.config) get_controller_status() (navigate.model.devices.APIs.sutter.MP285.MP285 method) get_current_position() (navigate.model.devices.APIs.sutter.MP285.MP285 method) get_data_buffer() (navigate.model.model.Model method) get_data_source() (in module navigate.model.data_sources) get_default_motor_axis_sequence() (navigate.model.devices.APIs.asi.asi_MFC_controller.MFCTwoThousand method) (navigate.model.devices.APIs.asi.asi_MS2000_controller.MS2000Controller method) (navigate.model.devices.APIs.asi.asi_tiger_controller.TigerController method) get_encoder_counts_per_mm() (navigate.model.devices.APIs.asi.asi_MFC_controller.MFCTwoThousand method) (navigate.model.devices.APIs.asi.asi_MS2000_controller.MS2000Controller method) (navigate.model.devices.APIs.asi.asi_tiger_controller.TigerController method) get_errors() (navigate.model.devices.APIs.omicron.LuxxLaser.LuxxLaser method) get_exposure_sweep_times() (navigate.model.microscope.Microscope method) get_ext_control() (navigate.model.devices.APIs.coherent.ObisLaser.ObisLaser method) get_feature_list() (navigate.model.model.Model method) get_frames_num (navigate.model.features.autofocus.Autofocus attribute) get_laser_model() (navigate.model.devices.APIs.coherent.ObisLaser.ObisLaser method) get_laser_operating_mode() (navigate.model.devices.APIs.coherent.ObisLaser.ObisLaser method) get_laser_power() (navigate.model.devices.APIs.coherent.ObisLaser.ObisLaser method) get_laser_status() (navigate.model.devices.APIs.coherent.ObisLaser.ObisLaser method) get_laser_wavelength() (navigate.model.devices.APIs.coherent.ObisLaser.ObisLaser method) get_line_interval() (navigate.model.devices.camera.base.CameraBase method) (navigate.model.devices.camera.hamamatsu.HamamatsuBase method) (navigate.model.devices.camera.hamamatsu.HamamatsuOrca method) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaFire method) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaFusion method) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaLightning method) (navigate.model.devices.camera.synthetic.SyntheticCamera method) get_maximum_laser_power() (navigate.model.devices.APIs.coherent.ObisLaser.ObisLaser method)

get_microscope_configuration_dict() (navigate.controller.configuration_controller.ConfigurationController method) get_microscope_info() (navigate.model.model.Model method) get_minimum_laser_power() (navigate.model.devices.APIs.coherent.ObisLaser.ObisLaser method) get_modal_coefs() (navigate.model.devices.mirrors.imop.ImagineOpticsMirror method) get_mode() (navigate.model.devices.APIs.omicron.LuxxLaser.LuxxLaser method) get_navigate_path() (in module navigate.config.config) get_new_frame() (navigate.model.devices.camera.hamamatsu.HamamatsuBase method) (navigate.model.devices.camera.hamamatsu.HamamatsuOrca method) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaFire method) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaFusion method) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaLightning method) (navigate.model.devices.camera.synthetic.SyntheticCamera method) get_offset_variance_maps() (navigate.model.devices.camera.base.CameraBase method) (navigate.model.devices.camera.hamamatsu.HamamatsuBase method) (navigate.model.devices.camera.hamamatsu.HamamatsuOrca method) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaFire method) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaFusion method) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaLightning method) (navigate.model.devices.camera.synthetic.SyntheticCamera method) (navigate.model.model.Model method) get_origin (navigate.model.features.common_features.ZStackAcquisition attribute) get_parameters() (navigate.model.devices.APIs.omicron.LuxxLaser.LuxxLaser method) get_position() (navigate.model.devices.APIs.asi.asi_MFC_controller.MFCTwoThousand method) (navigate.model.devices.APIs.asi.asi_MS2000_controller.MS2000Controller method) (navigate.model.devices.APIs.asi.asi_tiger_controller.TigerController method) get_position_dict() (navigate.model.devices.stages.asi.ASIStage method) (navigate.model.devices.stages.asi_MSTwoThousand.ASIStage method) (navigate.model.devices.stages.base.StageBase method) (navigate.model.devices.stages.mcl.MCLStage method) (navigate.model.devices.stages.pi.PIStage method) (navigate.model.devices.stages.sutter.SutterStage method) (navigate.model.devices.stages.synthetic.SyntheticStage method) (navigate.model.devices.stages.tl_kcube_inertial.TLKIMStage method) (navigate.model.devices.stages.tl_kcube_steppermotor.TLKSTStage method) get_power() (navigate.model.devices.APIs.omicron.LuxxLaser.LuxxLaser method) get_property_value() (navigate.model.devices.camera.synthetic.SyntheticCameraController static method) get_ram_info() (in module navigate.tools.file_functions) get_registered_funcs() (in module navigate.model.features.feature_container) get_result() (navigate.model.concurrency.concurrency_tools.CustodyThread method) (navigate.model.concurrency.concurrency_tools.ResultThread method) get_shape_from_metadata() (navigate.model.data_sources.bdv_data_source.BigDataViewerDataSource method) (navigate.model.data_sources.data_source.DataSource method) (navigate.model.data_sources.pyramidal_data_source.PyramidalDataSource method) (navigate.model.data_sources.tiff_data_source.TiffDataSource method) (navigate.model.data_sources.zarr_data_source.OMEZarrDataSource method) get_slice() (navigate.model.data_sources.bdv_data_source.BigDataViewerDataSource method) (navigate.model.data_sources.pyramidal_data_source.PyramidalDataSource method) (navigate.model.data_sources.zarr_data_source.OMEZarrDataSource method) get_speed() (navigate.model.devices.APIs.asi.asi_MFC_controller.MFCTwoThousand method) (navigate.model.devices.APIs.asi.asi_MS2000_controller.MS2000Controller method) (navigate.model.devices.APIs.asi.asi_tiger_controller.TigerController method) (navigate.model.devices.stages.asi.ASIStage method) (navigate.model.devices.stages.asi_MSTwoThousand.ASIStage method) (navigate.model.devices.stages.synthetic.SyntheticStage method) get_stage_position() (navigate.model.microscope.Microscope method) (navigate.model.model.Model method) get_stage_position_limits() (navigate.controller.configuration_controller.ConfigurationController method) get_steps() (navigate.model.features.adaptive_optics.TonyWilson method) (navigate.model.features.autofocus.Autofocus static method) (navigate.model.features.common_features.LoopByCount method) get_tw_frame_num() (navigate.model.features.adaptive_optics.TonyWilson method) get_waveform_template_parameters() (in module navigate.tools.waveform_template_funcs) get_zoom_value_list() (navigate.controller.configuration_controller.ConfigurationController method) getfield() (navigate.model.concurrency.concurrency_tools.SharedNDArray method) getName() (navigate.controller.thread_pool.SelfLockThread method) (navigate.model.concurrency.concurrency_tools.CustodyThread method) (navigate.model.concurrency.concurrency_tools.ResultThread method) getRunningThread() (navigate.controller.thread_pool.SynchronizedThreadPool method) globaltrace() (navigate.controller.thread_pool.SynchronizedThreadPool method) goal_position_offset (navigate.model.devices.zoom.dynamixel.DynamixelZoom attribute)

H

halt_filter_wheel() (navigate.model.devices.APIs.asi.asi_MFC_controller.MFCTwoThousand method) (navigate.model.devices.APIs.asi.asi_tiger_controller.TigerController method) HamamatsuBase (class in navigate.model.devices.camera.hamamatsu) HamamatsuOrca (class in navigate.model.devices.camera.hamamatsu) HamamatsuOrcaFire (class in navigate.model.devices.camera.hamamatsu) HamamatsuOrcaFusion (class in navigate.model.devices.camera.hamamatsu)

HamamatsuOrcaLightning (class in navigate.model.devices.camera.hamamatsu) handle (navigate.model.devices.stages.mcl.MCLStage attribute) has_tissue (navigate.model.features.volume_search.VolumeSearch attribute) has_tissue() (in module navigate.model.analysis.boundary_detect) has_tissue_queue (navigate.model.features.volume_search.VolumeSearch attribute) high_res_microscope_name (navigate.model.features.restful_features.IlastikSegmentation attribute) high_res_zoom_value (navigate.model.features.restful_features.IlastikSegmentation attribute)

I

id (navigate.model.devices.zoom.dynamixel.DynamixelZoom attribute) ident (navigate.controller.thread_pool.SelfLockThread property) (navigate.model.concurrency.concurrency_tools.CustodyThread property) (navigate.model.concurrency.concurrency_tools.ResultThread property) IlastikSegmentation (class in navigate.model.features.restful_features) imag (navigate.model.concurrency.concurrency_tools.SharedNDArray attribute) image (navigate.model.data_sources.bdv_data_source.BigDataViewerDataSource attribute) (navigate.model.data_sources.tiff_data_source.TiffDataSource attribute) image_count (navigate.model.model.Model attribute) image_writer (navigate.model.features.common_features.ZStackAcquisition attribute) (navigate.model.model.Model attribute) ImageWriter (class in navigate.model.features.image_writer) ImagineOpticsMirror (class in navigate.model.devices.mirrors.imop) imaging_mode (navigate.model.model.Model attribute) img_height (navigate.model.model.Model attribute) img_id (navigate.model.devices.camera.synthetic.SyntheticCamera attribute) img_width (navigate.model.model.Model attribute) in_data_func() (navigate.model.features.common_features.ZStackAcquisition method) in_func_data() (navigate.model.features.adaptive_optics.TonyWilson method) (navigate.model.features.auto_tile_scan.CalculateFocusRange method) (navigate.model.features.autofocus.Autofocus method) (navigate.model.features.remove_empty_tiles.DetectTissueInStack method) (navigate.model.features.remove_empty_tiles.DetectTissueInStackAndRecord method) (navigate.model.features.remove_empty_tiles.DetectTissueInStackAndReturn method) in_func_signal() (navigate.model.features.adaptive_optics.TonyWilson method) (navigate.model.features.auto_tile_scan.CalculateFocusRange method) (navigate.model.features.autofocus.Autofocus method) (navigate.model.features.remove_empty_tiles.DetectTissueInStack method) (navigate.model.features.remove_empty_tiles.DetectTissueInStackAndRecord method) (navigate.model.features.remove_empty_tiles.DetectTissueInStackAndReturn method) index() (navigate.model.features.feature_related_functions.SharedList method) info (navigate.model.microscope.Microscope attribute) init_data_func() (navigate.model.features.volume_search.VolumeSearch method) init_finished (navigate.model.devices.filter_wheel.sutter.SutterFilterWheel attribute) init_func() (navigate.model.features.restful_features.IlastikSegmentation method) init_pos (navigate.model.features.autofocus.Autofocus attribute) initialize_image_series() (navigate.model.devices.camera.hamamatsu.HamamatsuBase method) (navigate.model.devices.camera.hamamatsu.HamamatsuOrca method) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaFire method) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaFusion method) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaLightning method) (navigate.model.devices.camera.synthetic.SyntheticCamera method) initialize_laser() (navigate.model.devices.APIs.coherent.ObisLaser.ObisLaser method) (navigate.model.devices.APIs.omicron.LuxxLaser.LuxxLaser method) (navigate.model.devices.lasers.base.LaserBase method) (navigate.model.devices.lasers.synthetic.SyntheticLaser method) initialized (navigate.model.features.common_features.LoopByCount attribute) (navigate.model.features.common_features.MoveToNextPositionInMultiPositionTable attribute) injected_flag (navigate.model.model.Model attribute)

insert() (navigate.model.features.feature_related_functions.SharedList method) interrupt_move() (navigate.model.devices.APIs.sutter.MP285.MP285 method) is_acquiring (navigate.model.devices.camera.base.CameraBase attribute) (navigate.model.devices.camera.hamamatsu.HamamatsuBase attribute) (navigate.model.devices.camera.hamamatsu.HamamatsuOrca attribute) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaFire attribute) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaFusion attribute) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaLightning attribute) (navigate.model.devices.camera.synthetic.SyntheticCamera attribute) (navigate.model.model.Model attribute) is_alive() (navigate.controller.thread_pool.SelfLockThread method) (navigate.model.concurrency.concurrency_tools.CustodyThread method) (navigate.model.concurrency.concurrency_tools.ResultThread method) is_axis_busy() (navigate.model.devices.APIs.asi.asi_MFC_controller.MFCTwoThousand method) (navigate.model.devices.APIs.asi.asi_MS2000_controller.MS2000Controller method) (navigate.model.devices.APIs.asi.asi_tiger_controller.TigerController method) is_bigtiff (navigate.model.data_sources.tiff_data_source.TiffDataSource property) is_closed (navigate.model.features.feature_container.Container attribute) (navigate.model.features.feature_container.DataContainer attribute) (navigate.model.features.feature_container.SignalContainer attribute) is_device_busy() (navigate.model.devices.APIs.asi.asi_MFC_controller.MFCTwoThousand method) (navigate.model.devices.APIs.asi.asi_MS2000_controller.MS2000Controller method) (navigate.model.devices.APIs.asi.asi_tiger_controller.TigerController method) is_initialized (navigate.model.features.feature_container.DataNode attribute) (navigate.model.features.feature_container.SignalNode attribute) (navigate.model.features.feature_container.TreeNode attribute) is_interrupted (navigate.model.devices.APIs.sutter.MP285.MP285 attribute) is_live (navigate.model.model.Model attribute) is_marked (navigate.model.features.feature_container.DataNode attribute) is_moving (navigate.model.devices.APIs.sutter.MP285.MP285 attribute) is_moving() (navigate.model.devices.APIs.asi.asi_MFC_controller.MFCTwoThousand method) (navigate.model.devices.APIs.asi.asi_MS2000_controller.MS2000Controller method) (navigate.model.devices.APIs.asi.asi_tiger_controller.TigerController method) is_ome (navigate.model.data_sources.tiff_data_source.TiffDataSource property) is_open() (navigate.model.devices.APIs.asi.asi_MFC_controller.MFCTwoThousand method) (navigate.model.devices.APIs.asi.asi_MS2000_controller.MS2000Controller method) (navigate.model.devices.APIs.asi.asi_tiger_controller.TigerController method) is_save (navigate.model.model.Model attribute) is_synthetic (navigate.model.devices.mirrors.base.MirrorBase attribute) (navigate.model.devices.mirrors.imop.ImagineOpticsMirror attribute) (navigate.model.devices.mirrors.synthetic.SyntheticMirror attribute) (navigate.model.microscope.Microscope attribute) is_updating_analog_task (navigate.model.devices.daq.synthetic.SyntheticDAQ attribute) isDaemon() (navigate.controller.thread_pool.SelfLockThread method) (navigate.model.concurrency.concurrency_tools.CustodyThread method) (navigate.model.concurrency.concurrency_tools.ResultThread method) isLocked() (navigate.controller.thread_pool.SelfLockThread method) item() (navigate.model.concurrency.concurrency_tools.SharedNDArray method) itemset() (navigate.model.concurrency.concurrency_tools.SharedNDArray method) itemsize (navigate.model.concurrency.concurrency_tools.SharedNDArray attribute)

J

join() (navigate.controller.thread_pool.SelfLockThread method) (navigate.model.concurrency.concurrency_tools.CustodyThread method) (navigate.model.concurrency.concurrency_tools.ResultThread method)

K

key_len() (in module navigate.tools.slicing) killThreadInList() (navigate.controller.thread_pool.SynchronizedThreadPool method) kim_axes (navigate.model.devices.stages.tl_kcube_inertial.TLKIMStage attribute)

kim_controller (navigate.model.devices.stages.tl_kcube_inertial.TLKIMStage attribute) KST_axes (navigate.model.devices.stages.tl_kcube_steppermotor.TLKSTStage attribute) kst_controller (navigate.model.devices.stages.tl_kcube_steppermotor.TLKSTStage attribute)

L

laser (navigate.model.devices.APIs.coherent.ObisLaser.ObisLaser attribute) laser_wavelength (navigate.model.microscope.Microscope attribute) LaserBase (class in navigate.model.devices.lasers.base) lasers (navigate.model.microscope.Microscope attribute) lasers_info (navigate.controller.configuration_controller.ConfigurationController property) last_command_idx (navigate.model.devices.APIs.sutter.MP285.MP285 attribute) last_write_time (navigate.model.devices.APIs.sutter.MP285.MP285 attribute) launch_virtual_microscope() (navigate.model.model.Model method) load_and_start_devices() (navigate.model.microscope.Microscope method) load_camera_connection() (in module navigate.model.device_startup_functions) load_configs() (in module navigate.config.config) load_devices() (in module navigate.model.device_startup_functions) load_dynamic_parameter_functions() (in module navigate.model.features.feature_related_functions) load_feature_list_from_file() (navigate.model.model.Model method) load_feature_list_from_str() (navigate.model.model.Model method) load_feature_records() (navigate.model.model.Model method) load_features() (in module navigate.model.features.feature_container) load_filter_wheel_connection() (in module navigate.model.device_startup_functions) load_images() (navigate.model.devices.camera.synthetic.SyntheticCamera method) (navigate.model.model.Model method)

load_mirror() (in module navigate.model.device_startup_functions) load_module_from_file() (in module navigate.tools.common_functions) load_plugins() (navigate.model.plugins_model.PluginsModel method) load_plugins_through_manager() (navigate.model.plugins_model.PluginsModel method) load_sample() (navigate.model.devices.stages.synthetic.SyntheticStage method) load_stages() (in module navigate.model.device_startup_functions) load_yaml_file() (in module navigate.tools.file_functions) load_zoom_connection() (in module navigate.model.device_startup_functions) localtrace() (navigate.controller.thread_pool.SynchronizedThreadPool method) log_initialization() (in module navigate.tools.decorators) log_setup() (in module navigate.log_files.log_functions) logger (in module navigate.model.data_sources) (navigate.model.data_sources.bdv_data_source.BigDataViewerDataSource attribute) (navigate.model.data_sources.data_source.DataSource attribute) (navigate.model.data_sources.pyramidal_data_source.PyramidalDataSource attribute) (navigate.model.data_sources.tiff_data_source.TiffDataSource attribute) (navigate.model.data_sources.zarr_data_source.OMEZarrDataSource attribute) (navigate.model.model.Model attribute) LoopByCount (class in navigate.model.features.common_features) LUDLFilterWheel (class in navigate.model.devices.filter_wheel.ludl) LuxxLaser (class in navigate.model.devices.APIs.omicron.LuxxLaser)

M

main_process_listener() (in module navigate.log_files.log_functions) map_boundary() (in module navigate.model.analysis.boundary_detect) mark_position() (navigate.model.features.restful_features.IlastikSegmentation method) mark_saving_flags() (navigate.model.model.Model method) max() (navigate.model.concurrency.concurrency_tools.SharedNDArray method) max_entropy (navigate.model.features.autofocus.Autofocus attribute) (navigate.model.model.Model attribute) mcl_controller (navigate.model.devices.stages.mcl.MCLStage attribute) MCLStage (class in navigate.model.devices.stages.mcl) mean() (navigate.model.concurrency.concurrency_tools.SharedNDArray method) Metadata (class in navigate.model.metadata_sources.metadata) metadata (navigate.model.data_sources.bdv_data_source.BigDataViewerDataSource attribute) (navigate.model.data_sources.data_source.DataSource attribute) (navigate.model.data_sources.pyramidal_data_source.PyramidalDataSource attribute) (navigate.model.data_sources.tiff_data_source.TiffDataSource attribute) (navigate.model.data_sources.zarr_data_source.OMEZarrDataSource attribute) MFCTwoThousand (class in navigate.model.devices.APIs.asi.asi_MFC_controller) Microscope (class in navigate.model.microscope) microscope_config (navigate.controller.configuration_controller.ConfigurationController attribute) microscope_list (navigate.controller.configuration_controller.ConfigurationController property) microscope_name (navigate.controller.configuration_controller.ConfigurationController attribute) (navigate.model.devices.APIs.coherent.ObisLaser.ObisLaser attribute) (navigate.model.devices.APIs.omicron.LuxxLaser.LuxxLaser attribute) (navigate.model.devices.camera.base.CameraBase attribute) (navigate.model.devices.camera.hamamatsu.HamamatsuBase attribute) (navigate.model.devices.camera.hamamatsu.HamamatsuOrca attribute) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaFire attribute) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaFusion attribute) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaLightning attribute) (navigate.model.devices.camera.synthetic.SyntheticCamera attribute) (navigate.model.devices.daq.base.DAQBase attribute) (navigate.model.devices.daq.synthetic.SyntheticDAQ attribute) (navigate.model.devices.galvo.base.GalvoBase attribute) (navigate.model.devices.galvo.synthetic.SyntheticGalvo attribute) (navigate.model.devices.lasers.base.LaserBase attribute) (navigate.model.devices.lasers.synthetic.SyntheticLaser attribute) (navigate.model.devices.remote_focus.base.RemoteFocusBase attribute) (navigate.model.devices.remote_focus.equipment_solutions.RemoteFocusEquipmentSolutions attribute) (navigate.model.devices.remote_focus.ni.RemoteFocusNI attribute) (navigate.model.devices.remote_focus.synthetic.SyntheticRemoteFocus attribute) (navigate.model.devices.shutter.base.ShutterBase attribute) (navigate.model.devices.shutter.synthetic.SyntheticShutter attribute) (navigate.model.features.common_features.SetCameraParameters attribute) (navigate.model.features.image_writer.ImageWriter attribute) (navigate.model.microscope.Microscope attribute) microscopes (navigate.model.model.Model attribute) min() (navigate.model.concurrency.concurrency_tools.SharedNDArray method) min_image_height (navigate.model.devices.camera.base.CameraBase attribute) (navigate.model.devices.camera.hamamatsu.HamamatsuBase attribute) (navigate.model.devices.camera.hamamatsu.HamamatsuOrca attribute) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaFire attribute) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaFusion attribute) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaLightning attribute) (navigate.model.devices.camera.synthetic.SyntheticCamera attribute) min_image_width (navigate.model.devices.camera.base.CameraBase attribute) (navigate.model.devices.camera.hamamatsu.HamamatsuBase attribute) (navigate.model.devices.camera.hamamatsu.HamamatsuOrca attribute) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaFire attribute) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaFusion attribute) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaLightning attribute) (navigate.model.devices.camera.synthetic.SyntheticCamera attribute) minimum_exposure_time (navigate.model.devices.camera.base.CameraBase attribute) (navigate.model.devices.camera.hamamatsu.HamamatsuBase attribute) (navigate.model.devices.camera.hamamatsu.HamamatsuOrca attribute) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaFire attribute) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaFusion attribute) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaLightning attribute) (navigate.model.devices.camera.synthetic.SyntheticCamera attribute) mip (navigate.model.features.image_writer.ImageWriter attribute) mip_directory (navigate.model.features.image_writer.ImageWriter attribute) mirror_controller (navigate.model.devices.mirrors.base.MirrorBase attribute) (navigate.model.devices.mirrors.imop.ImagineOpticsMirror attribute) (navigate.model.devices.mirrors.synthetic.SyntheticMirror attribute) (navigate.model.features.adaptive_optics.TonyWilson attribute) mirror_parameters (navigate.model.devices.mirrors.base.MirrorBase attribute) (navigate.model.devices.mirrors.imop.ImagineOpticsMirror attribute) (navigate.model.devices.mirrors.synthetic.SyntheticMirror attribute) MirrorBase (class in navigate.model.devices.mirrors.base) mode (navigate.model.data_sources.bdv_data_source.BigDataViewerDataSource property) (navigate.model.data_sources.data_source.DataSource property) (navigate.model.data_sources.pyramidal_data_source.PyramidalDataSource property) (navigate.model.data_sources.tiff_data_source.TiffDataSource property) (navigate.model.data_sources.zarr_data_source.OMEZarrDataSource property) mode_names (navigate.model.features.adaptive_optics.TonyWilson attribute) Model (class in navigate.model.model) model (navigate.model.features.adaptive_optics.TonyWilson attribute) (navigate.model.features.auto_tile_scan.CalculateFocusRange attribute) (navigate.model.features.autofocus.Autofocus attribute) (navigate.model.features.common_features.ChangeResolution attribute) (navigate.model.features.common_features.FindTissueSimple2D attribute) (navigate.model.features.common_features.LoopByCount attribute) (navigate.model.features.common_features.MoveToNextPositionInMultiPositionTable attribute) (navigate.model.features.common_features.PrepareNextChannel attribute) (navigate.model.features.common_features.SetCameraParameters attribute) (navigate.model.features.common_features.Snap attribute) (navigate.model.features.common_features.WaitToContinue attribute) (navigate.model.features.common_features.ZStackAcquisition attribute) (navigate.model.features.remove_empty_tiles.DetectTissueInStack attribute) (navigate.model.features.remove_empty_tiles.DetectTissueInStackAndRecord attribute) (navigate.model.features.remove_empty_tiles.DetectTissueInStackAndReturn attribute) (navigate.model.features.remove_empty_tiles.RemoveEmptyPositions attribute) (navigate.model.features.restful_features.IlastikSegmentation attribute) (navigate.model.features.volume_search.VolumeSearch attribute) module navigate.config navigate.config.config navigate.config.configuration_database navigate.controller navigate.controller.configuration_controller navigate.controller.thread_pool navigate.log_files navigate.log_files.filters navigate.log_files.log_functions navigate.model navigate.model.analysis navigate.model.analysis.boundary_detect navigate.model.analysis.camera navigate.model.analysis.image_contrast navigate.model.concurrency navigate.model.concurrency.concurrency_tools navigate.model.data_sources navigate.model.data_sources.bdv_data_source navigate.model.data_sources.data_source navigate.model.data_sources.pyramidal_data_source navigate.model.data_sources.tiff_data_source navigate.model.data_sources.zarr_data_source navigate.model.device_startup_functions navigate.model.devices navigate.model.devices.APIs navigate.model.devices.APIs.asi navigate.model.devices.APIs.asi.asi_MFC_controller navigate.model.devices.APIs.asi.asi_MS2000_controller navigate.model.devices.APIs.asi.asi_tiger_controller navigate.model.devices.APIs.coherent navigate.model.devices.APIs.coherent.ObisLaser navigate.model.devices.APIs.dynamixel navigate.model.devices.APIs.dynamixel.dynamixel_functions navigate.model.devices.APIs.hamamatsu navigate.model.devices.APIs.imagineoptics navigate.model.devices.APIs.imagineoptics.enums navigate.model.devices.APIs.mcl navigate.model.devices.APIs.omicron navigate.model.devices.APIs.omicron.LuxxLaser navigate.model.devices.APIs.photometrics navigate.model.devices.APIs.sutter navigate.model.devices.APIs.sutter.MP285 navigate.model.devices.APIs.thorlabs navigate.model.devices.camera navigate.model.devices.camera.base navigate.model.devices.camera.hamamatsu navigate.model.devices.camera.synthetic navigate.model.devices.daq navigate.model.devices.daq.base navigate.model.devices.daq.synthetic navigate.model.devices.filter_wheel navigate.model.devices.filter_wheel.asi navigate.model.devices.filter_wheel.base navigate.model.devices.filter_wheel.ludl navigate.model.devices.filter_wheel.sutter navigate.model.devices.filter_wheel.synthetic navigate.model.devices.galvo navigate.model.devices.galvo.base navigate.model.devices.galvo.synthetic navigate.model.devices.lasers navigate.model.devices.lasers.base navigate.model.devices.lasers.synthetic navigate.model.devices.mirrors navigate.model.devices.mirrors.base navigate.model.devices.mirrors.imop navigate.model.devices.mirrors.synthetic navigate.model.devices.objectives navigate.model.devices.remote_focus navigate.model.devices.remote_focus.base navigate.model.devices.remote_focus.equipment_solutions navigate.model.devices.remote_focus.ni navigate.model.devices.remote_focus.synthetic navigate.model.devices.shutter navigate.model.devices.shutter.base navigate.model.devices.shutter.synthetic navigate.model.devices.stages navigate.model.devices.stages.asi navigate.model.devices.stages.asi_MFCTwoThousand navigate.model.devices.stages.asi_MSTwoThousand navigate.model.devices.stages.base navigate.model.devices.stages.mcl navigate.model.devices.stages.pi navigate.model.devices.stages.sutter navigate.model.devices.stages.synthetic navigate.model.devices.stages.tl_kcube_inertial navigate.model.devices.stages.tl_kcube_steppermotor navigate.model.devices.zoom navigate.model.devices.zoom.base navigate.model.devices.zoom.dynamixel navigate.model.devices.zoom.synthetic navigate.model.features navigate.model.features.adaptive_optics navigate.model.features.auto_tile_scan navigate.model.features.autofocus navigate.model.features.common_features navigate.model.features.feature_container navigate.model.features.feature_related_functions navigate.model.features.image_writer navigate.model.features.remove_empty_tiles navigate.model.features.restful_features navigate.model.features.volume_search navigate.model.metadata_sources navigate.model.metadata_sources.bdv_metadata navigate.model.metadata_sources.metadata navigate.model.metadata_sources.ome_tiff_metadata navigate.model.metadata_sources.zarr_metadata navigate.model.microscope navigate.model.model navigate.model.plugins_model navigate.model.waveforms navigate.tools navigate.tools.common_dict_tools navigate.tools.common_functions navigate.tools.decorators navigate.tools.file_functions navigate.tools.image navigate.tools.linear_algebra navigate.tools.main_functions navigate.tools.multipos_table_tools navigate.tools.sdf navigate.tools.slicing navigate.tools.waveform_template_funcs navigate.tools.xml_tools navigate.view navigate.view.custom_widgets navigate.view.main_window_content navigate.view.popups

move() (navigate.model.devices.APIs.asi.asi_MFC_controller.MFCTwoThousand method) (navigate.model.devices.APIs.asi.asi_MS2000_controller.MS2000Controller method) (navigate.model.devices.APIs.asi.asi_tiger_controller.TigerController method) (navigate.model.devices.remote_focus.equipment_solutions.RemoteFocusEquipmentSolutions method) (navigate.model.devices.remote_focus.ni.RemoteFocusNI method) (navigate.model.devices.remote_focus.synthetic.SyntheticRemoteFocus static method) (navigate.model.devices.zoom.base.ZoomBase method) (navigate.model.devices.zoom.dynamixel.DynamixelZoom method) (navigate.model.devices.zoom.synthetic.SyntheticZoom method) move_absolute() (navigate.model.devices.stages.asi.ASIStage method) (navigate.model.devices.stages.asi_MSTwoThousand.ASIStage method) (navigate.model.devices.stages.mcl.MCLStage method) (navigate.model.devices.stages.pi.PIStage method) (navigate.model.devices.stages.sutter.SutterStage method) (navigate.model.devices.stages.synthetic.SyntheticStage method) (navigate.model.devices.stages.tl_kcube_inertial.TLKIMStage method) (navigate.model.devices.stages.tl_kcube_steppermotor.TLKSTStage method) move_axis() (navigate.model.devices.APIs.asi.asi_MFC_controller.MFCTwoThousand method) (navigate.model.devices.APIs.asi.asi_MS2000_controller.MS2000Controller method) (navigate.model.devices.APIs.asi.asi_tiger_controller.TigerController method) move_axis_absolute() (navigate.model.devices.stages.asi.ASIStage method) (navigate.model.devices.stages.asi_MSTwoThousand.ASIStage method) (navigate.model.devices.stages.mcl.MCLStage method) (navigate.model.devices.stages.pi.PIStage method) (navigate.model.devices.stages.sutter.SutterStage method) (navigate.model.devices.stages.synthetic.SyntheticStage method) (navigate.model.devices.stages.tl_kcube_inertial.TLKIMStage method) (navigate.model.devices.stages.tl_kcube_steppermotor.TLKSTStage method) move_axis_relative() (navigate.model.devices.stages.asi_MSTwoThousand.ASIStage method) move_dichroic() (navigate.model.devices.APIs.asi.asi_MFC_controller.MFCTwoThousand method) (navigate.model.devices.APIs.asi.asi_tiger_controller.TigerController method) move_filter_wheel() (navigate.model.devices.APIs.asi.asi_MFC_controller.MFCTwoThousand method) (navigate.model.devices.APIs.asi.asi_tiger_controller.TigerController method) move_filter_wheel_to_home() (navigate.model.devices.APIs.asi.asi_MFC_controller.MFCTwoThousand method) (navigate.model.devices.APIs.asi.asi_tiger_controller.TigerController method) move_remote_focus() (navigate.model.microscope.Microscope method) move_stage() (navigate.model.microscope.Microscope method) (navigate.model.model.Model method) move_stage_offset() (navigate.model.microscope.Microscope method) move_to_position() (navigate.model.devices.stages.tl_kcube_steppermotor.TLKSTStage method) move_to_specified_position() (navigate.model.devices.APIs.sutter.MP285.MP285 method) moverel() (navigate.model.devices.APIs.asi.asi_MFC_controller.MFCTwoThousand method) (navigate.model.devices.APIs.asi.asi_MS2000_controller.MS2000Controller method) (navigate.model.devices.APIs.asi.asi_tiger_controller.TigerController method) moverel_axis() (navigate.model.devices.APIs.asi.asi_MFC_controller.MFCTwoThousand method) (navigate.model.devices.APIs.asi.asi_MS2000_controller.MS2000Controller method) (navigate.model.devices.APIs.asi.asi_tiger_controller.TigerController method) moveToDelete() (navigate.controller.thread_pool.SynchronizedThreadPool method) MoveToNextPositionInMultiPositionTable (class in navigate.model.features.common_features) MP285 (class in navigate.model.devices.APIs.sutter.MP285) ms2000_controller (navigate.model.devices.stages.asi_MSTwoThousand.ASIStage attribute) MS2000Controller (class in navigate.model.devices.APIs.asi.asi_MS2000_controller) MS2000Exception multiposition_table (navigate.model.features.common_features.MoveToNextPositionInMultiPositionTable attribute) multiscales_dict() (navigate.model.metadata_sources.zarr_metadata.OMEZarrMetadata method)

N

n_iter (navigate.model.features.adaptive_optics.TonyWilson attribute) n_modes (navigate.model.features.adaptive_optics.TonyWilson attribute) n_steps (navigate.model.features.adaptive_optics.TonyWilson attribute) n_waits (navigate.model.devices.APIs.sutter.MP285.MP285 attribute) name (navigate.controller.thread_pool.SelfLockThread property) (navigate.model.concurrency.concurrency_tools.CustodyThread property) (navigate.model.concurrency.concurrency_tools.ResultThread property) native_id (navigate.controller.thread_pool.SelfLockThread property) (navigate.model.concurrency.concurrency_tools.CustodyThread property) (navigate.model.concurrency.concurrency_tools.ResultThread property) navigate.config module navigate.config.config module navigate.config.configuration_database module navigate.controller module navigate.controller.configuration_controller module navigate.controller.thread_pool module navigate.log_files module navigate.log_files.filters module navigate.log_files.log_functions module navigate.model module navigate.model.analysis module navigate.model.analysis.boundary_detect module navigate.model.analysis.camera module navigate.model.analysis.image_contrast module navigate.model.concurrency module navigate.model.concurrency.concurrency_tools module navigate.model.data_sources module navigate.model.data_sources.bdv_data_source module navigate.model.data_sources.data_source module navigate.model.data_sources.pyramidal_data_source module navigate.model.data_sources.tiff_data_source module navigate.model.data_sources.zarr_data_source module navigate.model.device_startup_functions module navigate.model.devices module navigate.model.devices.APIs module navigate.model.devices.APIs.asi module navigate.model.devices.APIs.asi.asi_MFC_controller module navigate.model.devices.APIs.asi.asi_MS2000_controller module navigate.model.devices.APIs.asi.asi_tiger_controller module navigate.model.devices.APIs.coherent module navigate.model.devices.APIs.coherent.ObisLaser module navigate.model.devices.APIs.dynamixel module navigate.model.devices.APIs.dynamixel.dynamixel_functions module navigate.model.devices.APIs.hamamatsu module navigate.model.devices.APIs.imagineoptics module navigate.model.devices.APIs.imagineoptics.enums module navigate.model.devices.APIs.mcl module navigate.model.devices.APIs.omicron module navigate.model.devices.APIs.omicron.LuxxLaser module navigate.model.devices.APIs.photometrics module navigate.model.devices.APIs.sutter module navigate.model.devices.APIs.sutter.MP285 module navigate.model.devices.APIs.thorlabs module navigate.model.devices.camera module navigate.model.devices.camera.base module navigate.model.devices.camera.hamamatsu module navigate.model.devices.camera.synthetic module navigate.model.devices.daq module navigate.model.devices.daq.base module navigate.model.devices.daq.synthetic module navigate.model.devices.filter_wheel module navigate.model.devices.filter_wheel.asi module navigate.model.devices.filter_wheel.base module navigate.model.devices.filter_wheel.ludl module navigate.model.devices.filter_wheel.sutter module navigate.model.devices.filter_wheel.synthetic module navigate.model.devices.galvo module navigate.model.devices.galvo.base module navigate.model.devices.galvo.synthetic module navigate.model.devices.lasers module navigate.model.devices.lasers.base module navigate.model.devices.lasers.synthetic module navigate.model.devices.mirrors module navigate.model.devices.mirrors.base module navigate.model.devices.mirrors.imop module navigate.model.devices.mirrors.synthetic module navigate.model.devices.objectives module navigate.model.devices.remote_focus module navigate.model.devices.remote_focus.base module

navigate.model.devices.remote_focus.equipment_solutions module navigate.model.devices.remote_focus.ni module navigate.model.devices.remote_focus.synthetic module navigate.model.devices.shutter module navigate.model.devices.shutter.base module navigate.model.devices.shutter.synthetic module navigate.model.devices.stages module navigate.model.devices.stages.asi module navigate.model.devices.stages.asi_MFCTwoThousand module navigate.model.devices.stages.asi_MSTwoThousand module navigate.model.devices.stages.base module navigate.model.devices.stages.mcl module navigate.model.devices.stages.pi module navigate.model.devices.stages.sutter module navigate.model.devices.stages.synthetic module navigate.model.devices.stages.tl_kcube_inertial module navigate.model.devices.stages.tl_kcube_steppermotor module navigate.model.devices.zoom module navigate.model.devices.zoom.base module navigate.model.devices.zoom.dynamixel module navigate.model.devices.zoom.synthetic module navigate.model.features module navigate.model.features.adaptive_optics module navigate.model.features.auto_tile_scan module navigate.model.features.autofocus module navigate.model.features.common_features module navigate.model.features.feature_container module navigate.model.features.feature_related_functions module navigate.model.features.image_writer module navigate.model.features.remove_empty_tiles module navigate.model.features.restful_features module navigate.model.features.volume_search module navigate.model.metadata_sources module navigate.model.metadata_sources.bdv_metadata module navigate.model.metadata_sources.metadata module navigate.model.metadata_sources.ome_tiff_metadata module navigate.model.metadata_sources.zarr_metadata module navigate.model.microscope module navigate.model.model module navigate.model.plugins_model module navigate.model.waveforms module navigate.tools module navigate.tools.common_dict_tools module navigate.tools.common_functions module navigate.tools.decorators module navigate.tools.file_functions module navigate.tools.image module navigate.tools.linear_algebra module navigate.tools.main_functions module navigate.tools.multipos_table_tools module navigate.tools.sdf module navigate.tools.slicing module navigate.tools.waveform_template_funcs module navigate.tools.xml_tools module navigate.view module navigate.view.custom_widgets module navigate.view.main_window_content module navigate.view.popups module nbytes (navigate.model.concurrency.concurrency_tools.SharedNDArray attribute) (navigate.model.data_sources.bdv_data_source.BigDataViewerDataSource property) (navigate.model.data_sources.data_source.DataSource property) (navigate.model.data_sources.pyramidal_data_source.PyramidalDataSource property) (navigate.model.data_sources.tiff_data_source.TiffDataSource property) (navigate.model.data_sources.zarr_data_source.OMEZarrDataSource property) ndim (navigate.model.concurrency.concurrency_tools.SharedNDArray attribute) need_response (navigate.model.features.feature_container.DataNode attribute) (navigate.model.features.feature_container.SignalNode attribute) (navigate.model.features.feature_container.TreeNode attribute) need_to_move_new_position (navigate.model.features.common_features.ZStackAcquisition attribute) need_to_move_z_position (navigate.model.features.common_features.ZStackAcquisition attribute) new_position() (navigate.model.data_sources.zarr_data_source.OMEZarrDataSource method) newbyteorder() (navigate.model.concurrency.concurrency_tools.SharedNDArray method) node_funcs (navigate.model.features.feature_container.DataNode attribute) (navigate.model.features.feature_container.SignalNode attribute) (navigate.model.features.feature_container.TreeNode attribute) node_name (navigate.model.features.feature_container.DataNode attribute) (navigate.model.features.feature_container.SignalNode attribute) (navigate.model.features.feature_container.TreeNode attribute) node_type (navigate.model.features.feature_container.DataNode attribute) (navigate.model.features.feature_container.SignalNode attribute) (navigate.model.features.feature_container.TreeNode attribute) NonPerfFilter (class in navigate.log_files.filters) nonzero() (navigate.model.concurrency.concurrency_tools.SharedNDArray method) num_of_frame (navigate.model.devices.camera.synthetic.SyntheticCamera attribute) number_of_channels (navigate.controller.configuration_controller.ConfigurationController property) number_of_execution (navigate.model.features.feature_container.SignalContainer attribute) number_of_filter_wheels (navigate.controller.configuration_controller.ConfigurationController property) number_of_frames (navigate.model.features.image_writer.ImageWriter attribute) (navigate.model.microscope.Microscope attribute) (navigate.model.model.Model attribute) number_z_steps (navigate.model.features.common_features.ZStackAcquisition attribute)

O

ObisLaser (class in navigate.model.devices.APIs.coherent.ObisLaser) ObjectInSubprocess (class in navigate.model.concurrency.concurrency_tools) Objective (class in navigate.model.devices.objectives) offset (navigate.model.devices.camera.base.CameraBase property) (navigate.model.devices.camera.hamamatsu.HamamatsuBase property) (navigate.model.devices.camera.hamamatsu.HamamatsuOrca property) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaFire property) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaFusion property) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaLightning property) (navigate.model.devices.camera.synthetic.SyntheticCamera property) (navigate.model.features.common_features.MoveToNextPositionInMultiPositionTable attribute)

ome_tiff_xml_dict() (navigate.model.metadata_sources.ome_tiff_metadata.OMETIFFMetadata method) OMETIFFMetadata (class in navigate.model.metadata_sources.ome_tiff_metadata) OMEZarrDataSource (class in navigate.model.data_sources.zarr_data_source) OMEZarrMetadata (class in navigate.model.metadata_sources.zarr_metadata) open_shutter() (navigate.model.devices.shutter.base.ShutterBase method) (navigate.model.devices.shutter.synthetic.SyntheticShutter method) output_event_queue (navigate.model.microscope.Microscope attribute) overlap (navigate.model.features.common_features.FindTissueSimple2D attribute) (navigate.model.features.volume_search.VolumeSearch attribute) OWNDATA (navigate.model.concurrency.concurrency_tools.SharedNDArray attribute)

P

parity (navigate.model.devices.remote_focus.equipment_solutions.RemoteFocusEquipmentSolutions attribute) parse_xml() (in module navigate.tools.xml_tools) (navigate.model.metadata_sources.bdv_metadata.BigDataViewerMetadata method) partition() (navigate.model.concurrency.concurrency_tools.SharedNDArray method) pause_data_event (navigate.model.model.Model attribute) pause_data_lock (navigate.model.features.common_features.WaitToContinue attribute) pause_data_ready_lock (navigate.model.model.Model attribute) pause_data_thread() (navigate.model.model.Model method) pause_signal_lock (navigate.model.features.common_features.WaitToContinue attribute) per_stack (navigate.model.metadata_sources.bdv_metadata.BigDataViewerMetadata property) (navigate.model.metadata_sources.metadata.Metadata property) (navigate.model.metadata_sources.metadata.XMLMetadata property) (navigate.model.metadata_sources.ome_tiff_metadata.OMETIFFMetadata property) (navigate.model.metadata_sources.zarr_metadata.OMEZarrMetadata property) PerformanceFilter (class in navigate.log_files.filters) pi_axes (navigate.model.devices.stages.pi.PIStage attribute) pi_device (navigate.model.devices.stages.pi.PIStage attribute) pi_tools (navigate.model.devices.stages.pi.PIStage attribute) pieces_num (navigate.model.features.restful_features.IlastikSegmentation attribute) pieces_size (navigate.model.features.restful_features.IlastikSegmentation attribute) PIStage (class in navigate.model.devices.stages.pi) planes (navigate.model.features.remove_empty_tiles.DetectTissueInStack attribute) (navigate.model.features.remove_empty_tiles.DetectTissueInStackAndRecord attribute) (navigate.model.features.remove_empty_tiles.DetectTissueInStackAndReturn attribute) plot_data (navigate.model.features.autofocus.Autofocus attribute) plot_pipe (navigate.model.model.Model attribute) plugin_acquisition_modes (navigate.model.model.Model attribute) (navigate.model.plugins_model.PluginsModel attribute) plugin_devices (navigate.model.microscope.Microscope attribute) PluginsModel (class in navigate.model.plugins_model) PoliteThread (in module navigate.model.concurrency.concurrency_tools) poly2() (in module navigate.model.features.adaptive_optics) pop() (navigate.model.features.feature_related_functions.SharedList method) port_num (navigate.model.devices.zoom.dynamixel.DynamixelZoom attribute) position_count (navigate.model.features.common_features.MoveToNextPositionInMultiPositionTable attribute) position_records (navigate.model.features.remove_empty_tiles.DetectTissueInStackAndRecord attribute) (navigate.model.features.remove_empty_tiles.RemoveEmptyPositions attribute) positions (navigate.model.data_sources.bdv_data_source.BigDataViewerDataSource attribute) (navigate.model.data_sources.data_source.DataSource attribute) (navigate.model.data_sources.pyramidal_data_source.PyramidalDataSource attribute) (navigate.model.data_sources.tiff_data_source.TiffDataSource attribute) (navigate.model.data_sources.zarr_data_source.OMEZarrDataSource attribute) (navigate.model.features.common_features.ZStackAcquisition attribute) (navigate.model.metadata_sources.bdv_metadata.BigDataViewerMetadata attribute) (navigate.model.metadata_sources.metadata.Metadata attribute) (navigate.model.metadata_sources.metadata.XMLMetadata attribute) (navigate.model.metadata_sources.ome_tiff_metadata.OMETIFFMetadata attribute) (navigate.model.metadata_sources.zarr_metadata.OMEZarrMetadata attribute)

power_tent() (in module navigate.model.features.autofocus) pre_boundary (navigate.model.features.volume_search.VolumeSearch attribute) pre_data_func() (navigate.model.features.common_features.WaitToContinue method) (navigate.model.features.common_features.ZStackAcquisition method) pre_exposure_time (navigate.model.model.Model attribute) pre_frame_idx (navigate.model.devices.camera.synthetic.SyntheticCamera attribute) pre_func() (navigate.model.features.common_features.LoopByCount method) pre_func_data() (navigate.model.features.adaptive_optics.TonyWilson method) (navigate.model.features.auto_tile_scan.CalculateFocusRange method) (navigate.model.features.autofocus.Autofocus method) (navigate.model.features.remove_empty_tiles.DetectTissueInStack method) (navigate.model.features.remove_empty_tiles.DetectTissueInStackAndRecord method) (navigate.model.features.remove_empty_tiles.DetectTissueInStackAndReturn method) pre_func_signal() (navigate.model.features.adaptive_optics.TonyWilson method) (navigate.model.features.auto_tile_scan.CalculateFocusRange method) (navigate.model.features.autofocus.Autofocus method) (navigate.model.features.remove_empty_tiles.DetectTissueInStack method) (navigate.model.features.remove_empty_tiles.DetectTissueInStackAndRecord method) (navigate.model.features.remove_empty_tiles.DetectTissueInStackAndReturn method) pre_signal_func() (navigate.model.features.common_features.MoveToNextPositionInMultiPositionTable method) (navigate.model.features.common_features.WaitToContinue method) (navigate.model.features.common_features.ZStackAcquisition method) (navigate.model.features.volume_search.VolumeSearch method) pre_z (navigate.model.features.common_features.MoveToNextPositionInMultiPositionTable attribute) prepare_acquisition() (navigate.model.devices.daq.synthetic.SyntheticDAQ method) (navigate.model.microscope.Microscope method) (navigate.model.model.Model method) prepare_next_channel() (navigate.model.microscope.Microscope method) prepare_service() (in module navigate.model.features.restful_features) PrepareNextChannel (class in navigate.model.features.common_features) print_hex() (in module navigate.model.devices.APIs.omicron.LuxxLaser) process_data() (navigate.model.features.adaptive_optics.TonyWilson method) prod() (navigate.model.concurrency.concurrency_tools.SharedNDArray method) project_file (navigate.model.features.restful_features.IlastikSegmentation attribute) ptp() (navigate.model.concurrency.concurrency_tools.SharedNDArray method) put() (navigate.model.concurrency.concurrency_tools.SharedNDArray method) PyramidalDataSource (class in navigate.model.data_sources.pyramidal_data_source)

R

r_squared() (in module navigate.model.features.adaptive_optics) random_image (navigate.model.devices.camera.synthetic.SyntheticCamera attribute) ravel() (navigate.model.concurrency.concurrency_tools.SharedNDArray method) read() (navigate.model.data_sources.bdv_data_source.BigDataViewerDataSource method) (navigate.model.data_sources.data_source.DataSource method) (navigate.model.data_sources.pyramidal_data_source.PyramidalDataSource method) (navigate.model.data_sources.tiff_data_source.TiffDataSource method) (navigate.model.data_sources.zarr_data_source.OMEZarrDataSource method) (navigate.model.devices.APIs.omicron.LuxxLaser.LuxxLaser method) (navigate.model.devices.filter_wheel.sutter.SutterFilterWheel method) (navigate.model.devices.filter_wheel.synthetic.SyntheticFilterWheel method) read_bytes() (navigate.model.devices.remote_focus.equipment_solutions.RemoteFocusEquipmentSolutions method) read_on_init (navigate.model.devices.filter_wheel.sutter.SutterFilterWheel attribute) (navigate.model.devices.remote_focus.equipment_solutions.RemoteFocusEquipmentSolutions attribute) read_position() (navigate.model.devices.zoom.base.ZoomBase method) (navigate.model.devices.zoom.dynamixel.DynamixelZoom method) (navigate.model.devices.zoom.synthetic.SyntheticZoom method) read_response() (navigate.model.devices.APIs.asi.asi_MFC_controller.MFCTwoThousand method) (navigate.model.devices.APIs.asi.asi_MS2000_controller.MS2000Controller method) (navigate.model.devices.APIs.asi.asi_tiger_controller.TigerController method) (navigate.model.devices.APIs.sutter.MP285.MP285 method) readout_direction (navigate.model.features.common_features.SetCameraParameters attribute) real (navigate.model.concurrency.concurrency_tools.SharedNDArray attribute) refresh_display() (navigate.model.devices.APIs.sutter.MP285.MP285 method) register_acquisition_mode() (navigate.model.plugins_model.PluginsModel method) register_device() (navigate.model.plugins_model.PluginsModel method) register_feature_list() (navigate.model.plugins_model.PluginsModel method) registerResource() (navigate.controller.thread_pool.SynchronizedThreadPool method) release_pipe() (navigate.model.model.Model method) remaining_number_of_execution (navigate.model.features.feature_container.SignalContainer attribute) remote_focus_device (navigate.model.microscope.Microscope attribute) remote_focus_dict (navigate.controller.configuration_controller.ConfigurationController property) remote_focus_max_voltage (navigate.model.devices.remote_focus.base.RemoteFocusBase attribute) (navigate.model.devices.remote_focus.equipment_solutions.RemoteFocusEquipmentSolutions attribute) (navigate.model.devices.remote_focus.ni.RemoteFocusNI attribute) (navigate.model.devices.remote_focus.synthetic.SyntheticRemoteFocus attribute) remote_focus_min_voltage (navigate.model.devices.remote_focus.base.RemoteFocusBase attribute) (navigate.model.devices.remote_focus.equipment_solutions.RemoteFocusEquipmentSolutions attribute) (navigate.model.devices.remote_focus.ni.RemoteFocusNI attribute) (navigate.model.devices.remote_focus.synthetic.SyntheticRemoteFocus attribute) remote_focus_ramp() (in module navigate.model.waveforms) remote_focus_ramp_triangular() (in module navigate.model.waveforms) RemoteFocusBase (class in navigate.model.devices.remote_focus.base) RemoteFocusEquipmentSolutions (class in navigate.model.devices.remote_focus.equipment_solutions) RemoteFocusNI (class in navigate.model.devices.remote_focus.ni) remove() (navigate.model.features.feature_related_functions.SharedList method) RemoveEmptyPositions (class in navigate.model.features.remove_empty_tiles) removeThread() (navigate.controller.thread_pool.SynchronizedThreadPool method) repeat() (navigate.model.concurrency.concurrency_tools.SharedNDArray method) report (navigate.model.features.adaptive_optics.TonyWilson attribute) report_camera_settings() (navigate.model.microscope.Microscope method) report_position() (navigate.model.devices.stages.asi.ASIStage method) (navigate.model.devices.stages.asi_MSTwoThousand.ASIStage method) (navigate.model.devices.stages.mcl.MCLStage method) (navigate.model.devices.stages.pi.PIStage method) (navigate.model.devices.stages.sutter.SutterStage method) (navigate.model.devices.stages.synthetic.SyntheticStage method) (navigate.model.devices.stages.tl_kcube_inertial.TLKIMStage method) (navigate.model.devices.stages.tl_kcube_steppermotor.TLKSTStage method)

report_settings() (navigate.model.devices.camera.hamamatsu.HamamatsuBase method) (navigate.model.devices.camera.hamamatsu.HamamatsuOrca method) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaFire method) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaFusion method) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaLightning method) (navigate.model.devices.camera.synthetic.SyntheticCamera method) report_to_console() (navigate.model.devices.APIs.asi.asi_MFC_controller.MFCTwoThousand method) (navigate.model.devices.APIs.asi.asi_MS2000_controller.MS2000Controller method) (navigate.model.devices.APIs.asi.asi_tiger_controller.TigerController method) reset() (navigate.model.features.feature_container.Container method) (navigate.model.features.feature_container.DataContainer method) (navigate.model.features.feature_container.SignalContainer method) reset_controller() (navigate.model.devices.APIs.sutter.MP285.MP285 method) reset_feature_list() (navigate.model.model.Model method) reshape() (navigate.model.concurrency.concurrency_tools.SharedNDArray method) resize() (navigate.model.concurrency.concurrency_tools.SharedNDArray method) resolution (navigate.model.devices.APIs.sutter.MP285.MP285 attribute) (navigate.model.devices.stages.sutter.SutterStage attribute) (navigate.model.features.restful_features.IlastikSegmentation attribute) resolution_mode (navigate.model.features.common_features.ChangeResolution attribute) resolution_value (navigate.model.features.common_features.MoveToNextPositionInMultiPositionTable attribute) resolutions (navigate.model.data_sources.bdv_data_source.BigDataViewerDataSource property) (navigate.model.data_sources.pyramidal_data_source.PyramidalDataSource property) (navigate.model.data_sources.zarr_data_source.OMEZarrDataSource property) resources (navigate.controller.thread_pool.SynchronizedThreadPool attribute) ResultThread (class in navigate.model.concurrency.concurrency_tools) resume_data_thread() (navigate.model.model.Model method) ret_pos_dict (navigate.model.microscope.Microscope attribute) reverse() (navigate.model.features.feature_related_functions.SharedList method) robust_autofocus() (navigate.model.features.autofocus.Autofocus method) root (navigate.model.features.feature_container.Container attribute) (navigate.model.features.feature_container.DataContainer attribute) (navigate.model.features.feature_container.SignalContainer attribute) rotate_angle_x (navigate.model.metadata_sources.bdv_metadata.BigDataViewerMetadata attribute) rotate_angle_y (navigate.model.metadata_sources.bdv_metadata.BigDataViewerMetadata attribute) rotate_angle_z (navigate.model.metadata_sources.bdv_metadata.BigDataViewerMetadata attribute) rotate_data (navigate.model.metadata_sources.bdv_metadata.BigDataViewerMetadata attribute) rotate_transform (navigate.model.metadata_sources.bdv_metadata.BigDataViewerMetadata attribute) round() (navigate.model.concurrency.concurrency_tools.SharedNDArray method) run() (navigate.controller.thread_pool.SelfLockThread method) (navigate.model.concurrency.concurrency_tools.CustodyThread method) (navigate.model.concurrency.concurrency_tools.ResultThread method) (navigate.model.features.adaptive_optics.TonyWilson method) (navigate.model.features.autofocus.Autofocus method) (navigate.model.features.feature_container.DataContainer method) (navigate.model.features.feature_container.DataNode method) (navigate.model.features.feature_container.SignalContainer method) (navigate.model.features.feature_container.SignalNode method) run_acquisition() (navigate.model.devices.daq.synthetic.SyntheticDAQ method) (navigate.model.model.Model method) run_command() (navigate.model.microscope.Microscope method) (navigate.model.model.Model method) run_data_process() (navigate.model.model.Model method) run_homing() (navigate.model.devices.stages.tl_kcube_steppermotor.TLKSTStage method) run_live_acquisition() (navigate.model.model.Model method)

S

safe_to_write (navigate.model.devices.APIs.asi.asi_MFC_controller.MFCTwoThousand attribute) (navigate.model.devices.APIs.asi.asi_MS2000_controller.MS2000Controller attribute) (navigate.model.devices.APIs.asi.asi_tiger_controller.TigerController attribute) (navigate.model.devices.APIs.sutter.MP285.MP285 attribute) sample_rate (navigate.model.devices.daq.base.DAQBase attribute) (navigate.model.devices.daq.synthetic.SyntheticDAQ attribute) (navigate.model.devices.galvo.base.GalvoBase attribute) (navigate.model.devices.galvo.synthetic.SyntheticGalvo attribute) (navigate.model.devices.remote_focus.base.RemoteFocusBase attribute) (navigate.model.devices.remote_focus.equipment_solutions.RemoteFocusEquipmentSolutions attribute) (navigate.model.devices.remote_focus.ni.RemoteFocusNI attribute) (navigate.model.devices.remote_focus.synthetic.SyntheticRemoteFocus attribute) save_directory (navigate.model.data_sources.tiff_data_source.TiffDataSource attribute) (navigate.model.features.image_writer.ImageWriter attribute) save_image() (navigate.model.features.image_writer.ImageWriter method) save_report (navigate.model.features.adaptive_optics.TonyWilson attribute) save_wcs_file() (navigate.model.devices.mirrors.imop.ImagineOpticsMirror method) save_yaml_file() (in module navigate.tools.file_functions) saving_flag (navigate.model.features.common_features.Snap attribute) saving_flags (navigate.model.features.image_writer.ImageWriter attribute) sawtooth() (in module navigate.model.waveforms) scan_axis_triggered_move() (navigate.model.devices.stages.asi_MSTwoThousand.ASIStage method) scan_ports() (navigate.model.devices.APIs.asi.asi_MFC_controller.MFCTwoThousand static method) (navigate.model.devices.APIs.asi.asi_MS2000_controller.MS2000Controller static method) (navigate.model.devices.APIs.asi.asi_tiger_controller.TigerController static method) scanr() (navigate.model.devices.APIs.asi.asi_MFC_controller.MFCTwoThousand method) (navigate.model.devices.APIs.asi.asi_MS2000_controller.MS2000Controller method) (navigate.model.devices.APIs.asi.asi_tiger_controller.TigerController method) (navigate.model.devices.stages.asi.ASIStage method) (navigate.model.devices.stages.asi_MSTwoThousand.ASIStage method) (navigate.model.devices.stages.synthetic.SyntheticStage method) scanv() (navigate.model.devices.APIs.asi.asi_MFC_controller.MFCTwoThousand method) (navigate.model.devices.APIs.asi.asi_MS2000_controller.MS2000Controller method) (navigate.model.devices.APIs.asi.asi_tiger_controller.TigerController method) (navigate.model.devices.stages.asi.ASIStage method) (navigate.model.devices.stages.asi_MSTwoThousand.ASIStage method) searchsorted() (navigate.model.concurrency.concurrency_tools.SharedNDArray method) select_filter_wheel() (navigate.model.devices.APIs.asi.asi_MFC_controller.MFCTwoThousand method) (navigate.model.devices.APIs.asi.asi_tiger_controller.TigerController method) selfLock (navigate.controller.thread_pool.SelfLockThread attribute) SelfLockThread (class in navigate.controller.thread_pool) send_command() (navigate.model.devices.APIs.asi.asi_MFC_controller.MFCTwoThousand method) (navigate.model.devices.APIs.asi.asi_MS2000_controller.MS2000Controller method) (navigate.model.devices.APIs.asi.asi_tiger_controller.TigerController method) (navigate.model.devices.APIs.sutter.MP285.MP285 method) (navigate.model.devices.remote_focus.equipment_solutions.RemoteFocusEquipmentSolutions method) send_filter_wheel_command() (navigate.model.devices.APIs.asi.asi_MFC_controller.MFCTwoThousand method) (navigate.model.devices.APIs.asi.asi_tiger_controller.TigerController method) sensor_mode (navigate.model.features.common_features.SetCameraParameters attribute) serial (navigate.model.devices.APIs.sutter.MP285.MP285 attribute) (navigate.model.devices.filter_wheel.ludl.LUDLFilterWheel attribute) (navigate.model.devices.filter_wheel.sutter.SutterFilterWheel attribute) serial_number (navigate.model.devices.camera.hamamatsu.HamamatsuBase property) (navigate.model.devices.camera.hamamatsu.HamamatsuOrca property) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaFire property) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaFusion property) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaLightning property) (navigate.model.devices.camera.synthetic.SyntheticCamera attribute) (navigate.model.devices.stages.tl_kcube_inertial.TLKIMStage attribute) (navigate.model.devices.stages.tl_kcube_steppermotor.TLKSTStage attribute) serial_port (navigate.model.devices.APIs.asi.asi_MFC_controller.MFCTwoThousand attribute) (navigate.model.devices.APIs.asi.asi_MS2000_controller.MS2000Controller attribute) (navigate.model.devices.APIs.asi.asi_tiger_controller.TigerController attribute) SerialConnectionFactory (class in navigate.model.device_startup_functions) service_url (navigate.model.features.restful_features.IlastikSegmentation attribute) set_absolute_mode() (navigate.model.devices.APIs.sutter.MP285.MP285 method) set_autostart() (navigate.model.devices.APIs.omicron.LuxxLaser.LuxxLaser method) set_backlash() (navigate.model.devices.APIs.asi.asi_MFC_controller.MFCTwoThousand method) (navigate.model.devices.APIs.asi.asi_MS2000_controller.MS2000Controller method) (navigate.model.devices.APIs.asi.asi_tiger_controller.TigerController method) set_bigtiff() (navigate.model.data_sources.tiff_data_source.TiffDataSource method) set_binning() (navigate.model.devices.camera.hamamatsu.HamamatsuBase method) (navigate.model.devices.camera.hamamatsu.HamamatsuOrca method) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaFire method) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaFusion method) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaLightning method) (navigate.model.devices.camera.synthetic.SyntheticCamera method) set_camera_exposure_time() (navigate.model.microscope.Microscope method) set_camera_roi() (navigate.model.microscope.Microscope method) set_camera_sensor_mode() (navigate.model.microscope.Microscope method) set_error() (navigate.model.devices.APIs.asi.asi_MFC_controller.MFCTwoThousand method) (navigate.model.devices.APIs.asi.asi_MS2000_controller.MS2000Controller method) (navigate.model.devices.APIs.asi.asi_tiger_controller.TigerController method) set_exposure_time() (navigate.model.devices.camera.hamamatsu.HamamatsuBase method) (navigate.model.devices.camera.hamamatsu.HamamatsuOrca method) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaFire method) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaFusion method) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaLightning method) (navigate.model.devices.camera.synthetic.SyntheticCamera method) set_external_trigger() (navigate.model.devices.daq.synthetic.SyntheticDAQ method) set_feedback_alignment() (navigate.model.devices.APIs.asi.asi_MFC_controller.MFCTwoThousand method) (navigate.model.devices.APIs.asi.asi_MS2000_controller.MS2000Controller method) (navigate.model.devices.APIs.asi.asi_tiger_controller.TigerController method) set_filter() (navigate.model.devices.filter_wheel.asi.ASICubeSlider method) (navigate.model.devices.filter_wheel.asi.ASIFilterWheel method) (navigate.model.devices.filter_wheel.ludl.LUDLFilterWheel method) (navigate.model.devices.filter_wheel.sutter.SutterFilterWheel method) (navigate.model.devices.filter_wheel.synthetic.SyntheticFilterWheel method) set_finishing_accuracy() (navigate.model.devices.APIs.asi.asi_MFC_controller.MFCTwoThousand method) (navigate.model.devices.APIs.asi.asi_MS2000_controller.MS2000Controller method) (navigate.model.devices.APIs.asi.asi_tiger_controller.TigerController method) set_from_configuration_experiment() (navigate.model.metadata_sources.bdv_metadata.BigDataViewerMetadata method) (navigate.model.metadata_sources.metadata.Metadata method) (navigate.model.metadata_sources.metadata.XMLMetadata method) (navigate.model.metadata_sources.ome_tiff_metadata.OMETIFFMetadata method) (navigate.model.metadata_sources.zarr_metadata.OMEZarrMetadata method) set_from_dict() (navigate.model.metadata_sources.bdv_metadata.BigDataViewerMetadata method) (navigate.model.metadata_sources.metadata.Metadata method) (navigate.model.metadata_sources.metadata.XMLMetadata method) (navigate.model.metadata_sources.ome_tiff_metadata.OMETIFFMetadata method) (navigate.model.metadata_sources.zarr_metadata.OMEZarrMetadata method) set_from_wcs_file() (navigate.model.devices.mirrors.imop.ImagineOpticsMirror method) set_laser_operating_mode() (navigate.model.devices.APIs.coherent.ObisLaser.ObisLaser method) set_line_interval() (navigate.model.devices.camera.hamamatsu.HamamatsuBase method) (navigate.model.devices.camera.hamamatsu.HamamatsuOrca method) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaFire method) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaFusion method) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaLightning method) (navigate.model.devices.camera.synthetic.SyntheticCamera method) set_max_speed() (navigate.model.devices.APIs.asi.asi_MFC_controller.MFCTwoThousand method) (navigate.model.devices.APIs.asi.asi_MS2000_controller.MS2000Controller method) (navigate.model.devices.APIs.asi.asi_tiger_controller.TigerController method) set_metadata() (navigate.model.data_sources.bdv_data_source.BigDataViewerDataSource method) (navigate.model.data_sources.data_source.DataSource method) (navigate.model.data_sources.pyramidal_data_source.PyramidalDataSource method) (navigate.model.data_sources.tiff_data_source.TiffDataSource method) (navigate.model.data_sources.zarr_data_source.OMEZarrDataSource method) set_metadata_from_configuration_experiment() (navigate.model.data_sources.bdv_data_source.BigDataViewerDataSource method) (navigate.model.data_sources.data_source.DataSource method) (navigate.model.data_sources.pyramidal_data_source.PyramidalDataSource method) (navigate.model.data_sources.tiff_data_source.TiffDataSource method) (navigate.model.data_sources.zarr_data_source.OMEZarrDataSource method) set_mode() (navigate.model.devices.APIs.omicron.LuxxLaser.LuxxLaser method) set_positions_flat() (navigate.model.devices.mirrors.imop.ImagineOpticsMirror method) set_power() (navigate.model.devices.APIs.coherent.ObisLaser.ObisLaser method) (navigate.model.devices.APIs.omicron.LuxxLaser.LuxxLaser method) (navigate.model.devices.lasers.base.LaserBase method) (navigate.model.devices.lasers.synthetic.SyntheticLaser method) set_property() (navigate.model.features.feature_container.DataNode method) (navigate.model.features.feature_container.SignalNode method) (navigate.model.features.feature_container.TreeNode method) set_property_value() (navigate.model.devices.camera.synthetic.SyntheticCameraController static method) set_readout_direction() (navigate.model.devices.camera.base.CameraBase method) (navigate.model.devices.camera.hamamatsu.HamamatsuBase method) (navigate.model.devices.camera.hamamatsu.HamamatsuOrca method) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaFire method) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaFusion method) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaLightning method) (navigate.model.devices.camera.synthetic.SyntheticCamera method) set_resolution_and_velocity() (navigate.model.devices.APIs.sutter.MP285.MP285 method) set_ROI() (navigate.model.devices.camera.hamamatsu.HamamatsuBase method) (navigate.model.devices.camera.hamamatsu.HamamatsuOrca method) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaFire method) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaFusion method) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaLightning method) (navigate.model.devices.camera.synthetic.SyntheticCamera method) set_sensor_mode() (navigate.model.devices.camera.hamamatsu.HamamatsuBase method) (navigate.model.devices.camera.hamamatsu.HamamatsuOrca method) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaFire method) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaFusion method) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaLightning method) (navigate.model.devices.camera.synthetic.SyntheticCamera method) set_shape_from_configuration_experiment() (navigate.model.metadata_sources.bdv_metadata.BigDataViewerMetadata method) (navigate.model.metadata_sources.metadata.Metadata method) (navigate.model.metadata_sources.metadata.XMLMetadata method) (navigate.model.metadata_sources.ome_tiff_metadata.OMETIFFMetadata method) (navigate.model.metadata_sources.zarr_metadata.OMEZarrMetadata method) set_speed() (navigate.model.devices.APIs.asi.asi_MFC_controller.MFCTwoThousand method) (navigate.model.devices.APIs.asi.asi_MS2000_controller.MS2000Controller method) (navigate.model.devices.APIs.asi.asi_tiger_controller.TigerController method) (navigate.model.devices.stages.asi.ASIStage method) (navigate.model.devices.stages.asi_MSTwoThousand.ASIStage method) (navigate.model.devices.stages.synthetic.SyntheticStage method) set_speed_as_percent_max() (navigate.model.devices.APIs.asi.asi_MFC_controller.MFCTwoThousand method) (navigate.model.devices.APIs.asi.asi_MS2000_controller.MS2000Controller method) (navigate.model.devices.APIs.asi.asi_tiger_controller.TigerController method) set_stack_order_from_configuration_experiment() (navigate.model.metadata_sources.bdv_metadata.BigDataViewerMetadata method) (navigate.model.metadata_sources.metadata.Metadata method) (navigate.model.metadata_sources.metadata.XMLMetadata method) (navigate.model.metadata_sources.ome_tiff_metadata.OMETIFFMetadata method) (navigate.model.metadata_sources.zarr_metadata.OMEZarrMetadata method) set_triggered_move() (navigate.model.devices.APIs.asi.asi_MS2000_controller.MS2000Controller method) set_zoom() (navigate.model.devices.zoom.base.ZoomBase method) (navigate.model.devices.zoom.dynamixel.DynamixelZoom method) (navigate.model.devices.zoom.synthetic.SyntheticZoom method) SetCameraParameters (class in navigate.model.features.common_features) setDaemon() (navigate.controller.thread_pool.SelfLockThread method) (navigate.model.concurrency.concurrency_tools.CustodyThread method) (navigate.model.concurrency.concurrency_tools.ResultThread method) setfield() (navigate.model.concurrency.concurrency_tools.SharedNDArray method) setflags() (navigate.model.concurrency.concurrency_tools.SharedNDArray method) setName() (navigate.controller.thread_pool.SelfLockThread method) (navigate.model.concurrency.concurrency_tools.CustodyThread method) (navigate.model.concurrency.concurrency_tools.ResultThread method) setup() (navigate.model.data_sources.bdv_data_source.BigDataViewerDataSource method) (navigate.model.data_sources.data_source.DataSource method) (navigate.model.data_sources.pyramidal_data_source.PyramidalDataSource method) (navigate.model.data_sources.tiff_data_source.TiffDataSource method) (navigate.model.data_sources.zarr_data_source.OMEZarrDataSource method) shape (navigate.model.concurrency.concurrency_tools.SharedNDArray attribute) (navigate.model.data_sources.bdv_data_source.BigDataViewerDataSource property) (navigate.model.data_sources.data_source.DataSource property) (navigate.model.data_sources.pyramidal_data_source.PyramidalDataSource property) (navigate.model.data_sources.tiff_data_source.TiffDataSource property) (navigate.model.data_sources.zarr_data_source.OMEZarrDataSource property) (navigate.model.metadata_sources.bdv_metadata.BigDataViewerMetadata property) (navigate.model.metadata_sources.metadata.Metadata property) (navigate.model.metadata_sources.metadata.XMLMetadata property) (navigate.model.metadata_sources.ome_tiff_metadata.OMETIFFMetadata property) (navigate.model.metadata_sources.zarr_metadata.OMEZarrMetadata property) shape_c (navigate.model.data_sources.bdv_data_source.BigDataViewerDataSource attribute) (navigate.model.data_sources.data_source.DataSource attribute) (navigate.model.data_sources.pyramidal_data_source.PyramidalDataSource attribute) (navigate.model.data_sources.tiff_data_source.TiffDataSource attribute) (navigate.model.data_sources.zarr_data_source.OMEZarrDataSource attribute) (navigate.model.metadata_sources.bdv_metadata.BigDataViewerMetadata attribute) (navigate.model.metadata_sources.metadata.Metadata attribute) (navigate.model.metadata_sources.metadata.XMLMetadata attribute) (navigate.model.metadata_sources.ome_tiff_metadata.OMETIFFMetadata attribute) (navigate.model.metadata_sources.zarr_metadata.OMEZarrMetadata attribute) shape_t (navigate.model.data_sources.bdv_data_source.BigDataViewerDataSource attribute) (navigate.model.data_sources.data_source.DataSource attribute) (navigate.model.data_sources.pyramidal_data_source.PyramidalDataSource attribute) (navigate.model.data_sources.tiff_data_source.TiffDataSource attribute) (navigate.model.data_sources.zarr_data_source.OMEZarrDataSource attribute) (navigate.model.metadata_sources.bdv_metadata.BigDataViewerMetadata attribute) (navigate.model.metadata_sources.metadata.Metadata attribute) (navigate.model.metadata_sources.metadata.XMLMetadata attribute) (navigate.model.metadata_sources.ome_tiff_metadata.OMETIFFMetadata attribute) (navigate.model.metadata_sources.zarr_metadata.OMEZarrMetadata attribute)

shape_x (navigate.model.data_sources.bdv_data_source.BigDataViewerDataSource attribute) (navigate.model.data_sources.data_source.DataSource attribute) (navigate.model.data_sources.pyramidal_data_source.PyramidalDataSource attribute) (navigate.model.data_sources.tiff_data_source.TiffDataSource attribute) (navigate.model.data_sources.zarr_data_source.OMEZarrDataSource attribute) (navigate.model.metadata_sources.bdv_metadata.BigDataViewerMetadata attribute) (navigate.model.metadata_sources.metadata.Metadata attribute) (navigate.model.metadata_sources.metadata.XMLMetadata attribute) (navigate.model.metadata_sources.ome_tiff_metadata.OMETIFFMetadata attribute) (navigate.model.metadata_sources.zarr_metadata.OMEZarrMetadata attribute) shape_y (navigate.model.data_sources.bdv_data_source.BigDataViewerDataSource attribute) (navigate.model.data_sources.data_source.DataSource attribute) (navigate.model.data_sources.pyramidal_data_source.PyramidalDataSource attribute) (navigate.model.data_sources.tiff_data_source.TiffDataSource attribute) (navigate.model.data_sources.zarr_data_source.OMEZarrDataSource attribute) (navigate.model.metadata_sources.bdv_metadata.BigDataViewerMetadata attribute) (navigate.model.metadata_sources.metadata.Metadata attribute) (navigate.model.metadata_sources.metadata.XMLMetadata attribute) (navigate.model.metadata_sources.ome_tiff_metadata.OMETIFFMetadata attribute) (navigate.model.metadata_sources.zarr_metadata.OMEZarrMetadata attribute) shape_z (navigate.model.data_sources.bdv_data_source.BigDataViewerDataSource attribute) (navigate.model.data_sources.data_source.DataSource attribute) (navigate.model.data_sources.pyramidal_data_source.PyramidalDataSource attribute) (navigate.model.data_sources.tiff_data_source.TiffDataSource attribute) (navigate.model.data_sources.zarr_data_source.OMEZarrDataSource attribute) (navigate.model.metadata_sources.bdv_metadata.BigDataViewerMetadata attribute) (navigate.model.metadata_sources.metadata.Metadata attribute) (navigate.model.metadata_sources.metadata.XMLMetadata attribute) (navigate.model.metadata_sources.ome_tiff_metadata.OMETIFFMetadata attribute) (navigate.model.metadata_sources.zarr_metadata.OMEZarrMetadata attribute) shapes (navigate.model.data_sources.bdv_data_source.BigDataViewerDataSource property) (navigate.model.data_sources.pyramidal_data_source.PyramidalDataSource property) (navigate.model.data_sources.zarr_data_source.OMEZarrDataSource property) SharedList (class in navigate.model.features.feature_related_functions) SharedNDArray (class in navigate.model.concurrency.concurrency_tools) shear_angle (navigate.model.metadata_sources.bdv_metadata.BigDataViewerMetadata attribute) shear_data (navigate.model.metadata_sources.bdv_metadata.BigDataViewerMetadata attribute) shear_dimension (navigate.model.metadata_sources.bdv_metadata.BigDataViewerMetadata attribute) shear_transform (navigate.model.metadata_sources.bdv_metadata.BigDataViewerMetadata attribute) show_img_pipe (navigate.model.model.Model attribute) shutter (navigate.model.microscope.Microscope attribute) shutter_state (navigate.model.devices.shutter.base.ShutterBase attribute) (navigate.model.devices.shutter.synthetic.SyntheticShutter attribute) ShutterBase (class in navigate.model.devices.shutter.base) sign() (in module navigate.tools.multipos_table_tools) signal_end() (navigate.model.features.common_features.ZStackAcquisition method) (navigate.model.features.volume_search.VolumeSearch method) signal_func() (navigate.model.features.common_features.ChangeResolution method) (navigate.model.features.common_features.LoopByCount method) (navigate.model.features.common_features.MoveToNextPositionInMultiPositionTable method) (navigate.model.features.common_features.PrepareNextChannel method) (navigate.model.features.common_features.SetCameraParameters method) (navigate.model.features.common_features.Snap method) (navigate.model.features.common_features.StackPause method) (navigate.model.features.common_features.WaitToContinue method) (navigate.model.features.common_features.ZStackAcquisition method) (navigate.model.features.remove_empty_tiles.RemoveEmptyPositions method) (navigate.model.features.volume_search.VolumeSearch method) signal_id (navigate.model.features.autofocus.Autofocus attribute) signal_response_func() (navigate.model.features.remove_empty_tiles.DetectTissueInStackAndReturn method) (navigate.model.features.volume_search.VolumeSearch method) signal_thread (navigate.model.model.Model attribute) SignalContainer (class in navigate.model.features.feature_container) SignalNode (class in navigate.model.features.feature_container) signals (navigate.model.features.common_features.LoopByCount attribute) simplified_data_process() (navigate.model.model.Model method) sine_wave() (in module navigate.model.waveforms) single_pulse() (in module navigate.model.waveforms) sinx (navigate.model.features.volume_search.VolumeSearch attribute) siny (navigate.model.features.volume_search.VolumeSearch attribute) sio (navigate.model.devices.filter_wheel.ludl.LUDLFilterWheel attribute) size (navigate.model.concurrency.concurrency_tools.SharedNDArray attribute) sleeptime (navigate.model.devices.zoom.dynamixel.DynamixelZoom attribute) slice_len() (in module navigate.tools.slicing) smart_ask() (navigate.model.devices.APIs.omicron.LuxxLaser.LuxxLaser method) smooth_waveform() (in module navigate.model.waveforms) Snap (class in navigate.model.features.common_features) snap_image() (navigate.model.model.Model method) sort() (navigate.model.concurrency.concurrency_tools.SharedNDArray method) (navigate.model.features.feature_related_functions.SharedList method) speed (navigate.model.devices.APIs.sutter.MP285.MP285 attribute) (navigate.model.devices.filter_wheel.sutter.SutterFilterWheel attribute) (navigate.model.devices.stages.sutter.SutterStage attribute) sphere() (in module navigate.tools.sdf) square() (in module navigate.model.waveforms) squeeze() (navigate.model.concurrency.concurrency_tools.SharedNDArray method) stack_cycling_mode (navigate.model.features.common_features.ZStackAcquisition attribute) StackPause (class in navigate.model.features.common_features) stage (navigate.model.devices.stages.sutter.SutterStage attribute) stage_default_position (navigate.controller.configuration_controller.ConfigurationController property) stage_distance_threshold (navigate.model.features.common_features.MoveToNextPositionInMultiPositionTable attribute) stage_feedback (navigate.model.devices.stages.asi.ASIStage attribute) (navigate.model.devices.stages.asi_MSTwoThousand.ASIStage attribute) (navigate.model.devices.stages.base.StageBase attribute) (navigate.model.devices.stages.mcl.MCLStage attribute) (navigate.model.devices.stages.pi.PIStage attribute) (navigate.model.devices.stages.sutter.SutterStage attribute) (navigate.model.devices.stages.synthetic.SyntheticStage attribute) (navigate.model.devices.stages.tl_kcube_inertial.TLKIMStage attribute) (navigate.model.devices.stages.tl_kcube_steppermotor.TLKSTStage attribute) stage_flip_flags (navigate.controller.configuration_controller.ConfigurationController property) stage_limits (navigate.model.devices.stages.asi.ASIStage attribute) (navigate.model.devices.stages.asi_MSTwoThousand.ASIStage attribute) (navigate.model.devices.stages.base.StageBase attribute) (navigate.model.devices.stages.mcl.MCLStage attribute) (navigate.model.devices.stages.pi.PIStage attribute) (navigate.model.devices.stages.sutter.SutterStage attribute) (navigate.model.devices.stages.synthetic.SyntheticStage attribute) (navigate.model.devices.stages.tl_kcube_inertial.TLKIMStage attribute) (navigate.model.devices.stages.tl_kcube_steppermotor.TLKSTStage attribute) stage_positions_to_affine_matrix() (navigate.model.metadata_sources.bdv_metadata.BigDataViewerMetadata method) stage_setting_dict (navigate.controller.configuration_controller.ConfigurationController property) stage_step (navigate.controller.configuration_controller.ConfigurationController property) stage_x_pos (navigate.model.devices.stages.sutter.SutterStage attribute) stage_y_pos (navigate.model.devices.stages.sutter.SutterStage attribute) stage_z_pos (navigate.model.devices.stages.sutter.SutterStage attribute) StageBase (class in navigate.model.devices.stages.base) stages (navigate.model.microscope.Microscope attribute) stages_list (navigate.model.microscope.Microscope attribute) start() (navigate.controller.thread_pool.SelfLockThread method) (navigate.model.concurrency.concurrency_tools.CustodyThread method) (navigate.model.concurrency.concurrency_tools.ResultThread method) (navigate.model.devices.APIs.omicron.LuxxLaser.LuxxLaser method) start_camera() (in module navigate.model.device_startup_functions) start_daq() (in module navigate.model.device_startup_functions) start_filter_wheel() (in module navigate.model.device_startup_functions) start_focus (navigate.model.features.common_features.ZStackAcquisition attribute) start_galvo() (in module navigate.model.device_startup_functions) start_lasers() (in module navigate.model.device_startup_functions) start_mirror() (in module navigate.model.device_startup_functions) start_remote_focus_device() (in module navigate.model.device_startup_functions) start_scan() (navigate.model.devices.APIs.asi.asi_MFC_controller.MFCTwoThousand method) (navigate.model.devices.APIs.asi.asi_MS2000_controller.MS2000Controller method) (navigate.model.devices.APIs.asi.asi_tiger_controller.TigerController method) (navigate.model.devices.stages.asi.ASIStage method) (navigate.model.devices.stages.asi_MSTwoThousand.ASIStage method) (navigate.model.devices.stages.synthetic.SyntheticStage method) start_shutter() (in module navigate.model.device_startup_functions) start_stage() (in module navigate.model.device_startup_functions) start_tasks() (navigate.model.devices.daq.synthetic.SyntheticDAQ method) start_time (navigate.model.model.Model attribute) start_z_position (navigate.model.features.common_features.ZStackAcquisition attribute) start_zoom() (in module navigate.model.device_startup_functions) state (navigate.model.devices.shutter.base.ShutterBase property) (navigate.model.devices.shutter.synthetic.SyntheticShutter property) std() (navigate.model.concurrency.concurrency_tools.SharedNDArray method) step_by_frame (navigate.model.features.common_features.LoopByCount attribute) step_image_height (navigate.model.devices.camera.base.CameraBase attribute) (navigate.model.devices.camera.hamamatsu.HamamatsuBase attribute) (navigate.model.devices.camera.hamamatsu.HamamatsuOrca attribute) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaFire attribute) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaFusion attribute) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaLightning attribute) (navigate.model.devices.camera.synthetic.SyntheticCamera attribute) step_image_width (navigate.model.devices.camera.base.CameraBase attribute) (navigate.model.devices.camera.hamamatsu.HamamatsuBase attribute) (navigate.model.devices.camera.hamamatsu.HamamatsuOrca attribute) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaFire attribute) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaFusion attribute) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaLightning attribute) (navigate.model.devices.camera.synthetic.SyntheticCamera attribute) steps (navigate.model.features.common_features.LoopByCount attribute) stop() (navigate.model.devices.APIs.asi.asi_MFC_controller.MFCTwoThousand method) (navigate.model.devices.APIs.asi.asi_MS2000_controller.MS2000Controller method) (navigate.model.devices.APIs.asi.asi_tiger_controller.TigerController method) (navigate.model.devices.APIs.omicron.LuxxLaser.LuxxLaser method) (navigate.model.devices.stages.asi.ASIStage method) (navigate.model.devices.stages.asi_MSTwoThousand.ASIStage method) (navigate.model.devices.stages.base.StageBase method) (navigate.model.devices.stages.mcl.MCLStage method) (navigate.model.devices.stages.pi.PIStage method) (navigate.model.devices.stages.sutter.SutterStage method) (navigate.model.devices.stages.synthetic.SyntheticStage method) (navigate.model.devices.stages.tl_kcube_inertial.TLKIMStage method) (navigate.model.devices.stages.tl_kcube_steppermotor.TLKSTStage method) stop_acquisition (navigate.model.model.Model attribute) stop_acquisition() (navigate.model.devices.daq.synthetic.SyntheticDAQ method) stop_bits (navigate.model.devices.remote_focus.equipment_solutions.RemoteFocusEquipmentSolutions attribute) stop_scan() (navigate.model.devices.APIs.asi.asi_MFC_controller.MFCTwoThousand method) (navigate.model.devices.APIs.asi.asi_MS2000_controller.MS2000Controller method) (navigate.model.devices.APIs.asi.asi_tiger_controller.TigerController method) (navigate.model.devices.stages.asi.ASIStage method) (navigate.model.devices.stages.asi_MSTwoThousand.ASIStage method) (navigate.model.devices.stages.synthetic.SyntheticStage method) stop_send_signal (navigate.model.model.Model attribute) stop_stage() (navigate.model.microscope.Microscope method) (navigate.model.model.Model method) stop_tasks() (navigate.model.devices.daq.synthetic.SyntheticDAQ method) stopwatch() (in module navigate.model.devices.APIs.omicron.LuxxLaser) strides (navigate.model.concurrency.concurrency_tools.SharedNDArray attribute) sub_dir (navigate.model.features.image_writer.ImageWriter attribute) subdivisions (navigate.model.data_sources.bdv_data_source.BigDataViewerDataSource property) (navigate.model.data_sources.pyramidal_data_source.PyramidalDataSource property) (navigate.model.data_sources.zarr_data_source.OMEZarrDataSource property) sum() (navigate.model.concurrency.concurrency_tools.SharedNDArray method) SutterFilterWheel (class in navigate.model.devices.filter_wheel.sutter) SutterStage (class in navigate.model.devices.stages.sutter) swapaxes() (navigate.model.concurrency.concurrency_tools.SharedNDArray method) sweep_time (navigate.model.devices.galvo.base.GalvoBase attribute) (navigate.model.devices.galvo.synthetic.SyntheticGalvo attribute) (navigate.model.devices.remote_focus.base.RemoteFocusBase attribute) (navigate.model.devices.remote_focus.equipment_solutions.RemoteFocusEquipmentSolutions attribute) (navigate.model.devices.remote_focus.ni.RemoteFocusNI attribute) (navigate.model.devices.remote_focus.synthetic.SyntheticRemoteFocus attribute) sweep_times (navigate.model.devices.daq.base.DAQBase attribute) (navigate.model.devices.daq.synthetic.SyntheticDAQ attribute) SynchronizedThreadPool (class in navigate.controller.thread_pool) SyntheticCamera (class in navigate.model.devices.camera.synthetic) SyntheticCameraController (class in navigate.model.devices.camera.synthetic) SyntheticDAQ (class in navigate.model.devices.daq.synthetic) SyntheticFilterWheel (class in navigate.model.devices.filter_wheel.synthetic) SyntheticGalvo (class in navigate.model.devices.galvo.synthetic) SyntheticLaser (class in navigate.model.devices.lasers.synthetic) SyntheticMirror (class in navigate.model.devices.mirrors.synthetic) SyntheticRemoteFocus (class in navigate.model.devices.remote_focus.synthetic) SyntheticShutter (class in navigate.model.devices.shutter.synthetic) SyntheticStage (class in navigate.model.devices.stages.synthetic) SyntheticZoom (class in navigate.model.devices.zoom.synthetic)

T

T (navigate.model.concurrency.concurrency_tools.SharedNDArray attribute) take() (navigate.model.concurrency.concurrency_tools.SharedNDArray method) target_channel (navigate.model.features.autofocus.Autofocus attribute) target_frame_id (navigate.model.features.autofocus.Autofocus attribute) target_resolution (navigate.model.features.common_features.FindTissueSimple2D attribute) (navigate.model.features.volume_search.VolumeSearch attribute) target_zoom (navigate.model.features.common_features.FindTissueSimple2D attribute) (navigate.model.features.volume_search.VolumeSearch attribute) terminate() (navigate.model.microscope.Microscope method) (navigate.model.model.Model method) text_array() (in module navigate.tools.image) threadTaskWrapping() (navigate.controller.thread_pool.SynchronizedThreadPool method) ThreadWaitlist (class in navigate.controller.thread_pool) tif_images (navigate.model.devices.camera.synthetic.SyntheticCamera attribute) TiffDataSource (class in navigate.model.data_sources.tiff_data_source) TigerController (class in navigate.model.devices.APIs.asi.asi_tiger_controller) TigerException timeout (in module navigate.model.devices.filter_wheel.ludl) (in module navigate.model.devices.filter_wheel.sutter) (navigate.model.devices.APIs.coherent.ObisLaser.ObisLaser attribute) (navigate.model.devices.remote_focus.equipment_solutions.RemoteFocusEquipmentSolutions attribute) (navigate.model.devices.zoom.dynamixel.DynamixelZoom attribute) TLKIMStage (class in navigate.model.devices.stages.tl_kcube_inertial) TLKSTStage (class in navigate.model.devices.stages.tl_kcube_steppermotor) to_xml() (navigate.model.metadata_sources.bdv_metadata.BigDataViewerMetadata method) (navigate.model.metadata_sources.metadata.XMLMetadata method) (navigate.model.metadata_sources.ome_tiff_metadata.OMETIFFMetadata method) tobytes() (navigate.model.concurrency.concurrency_tools.SharedNDArray method)

toDeleteList (navigate.controller.thread_pool.SynchronizedThreadPool attribute) tofile() (navigate.model.concurrency.concurrency_tools.SharedNDArray method) tolist() (navigate.model.concurrency.concurrency_tools.SharedNDArray method) TonyWilson (class in navigate.model.features.adaptive_optics) top_command_idx (navigate.model.devices.APIs.sutter.MP285.MP285 attribute) torque_disable (navigate.model.devices.zoom.dynamixel.DynamixelZoom attribute) torque_enable (navigate.model.devices.zoom.dynamixel.DynamixelZoom attribute) tostring() (navigate.model.concurrency.concurrency_tools.SharedNDArray method) total_acquisition_count (navigate.model.model.Model attribute) total_frame_num (navigate.model.features.autofocus.Autofocus attribute) total_image_count (navigate.model.model.Model attribute) trace() (navigate.model.concurrency.concurrency_tools.SharedNDArray method) transpose() (navigate.model.concurrency.concurrency_tools.SharedNDArray method) TreeNode (class in navigate.model.features.feature_container) trigger_mode (navigate.model.devices.daq.synthetic.SyntheticDAQ attribute) trigger_source (navigate.model.devices.remote_focus.equipment_solutions.RemoteFocusEquipmentSolutions attribute) (navigate.model.devices.remote_focus.ni.RemoteFocusNI attribute) turn_off() (navigate.model.devices.APIs.coherent.ObisLaser.ObisLaser method) (navigate.model.devices.APIs.omicron.LuxxLaser.LuxxLaser method) (navigate.model.devices.galvo.base.GalvoBase method) (navigate.model.devices.galvo.synthetic.SyntheticGalvo method) (navigate.model.devices.lasers.base.LaserBase method) (navigate.model.devices.lasers.synthetic.SyntheticLaser method) turn_off_lasers() (navigate.model.microscope.Microscope method) turn_on() (navigate.model.devices.APIs.coherent.ObisLaser.ObisLaser method) (navigate.model.devices.APIs.omicron.LuxxLaser.LuxxLaser method) (navigate.model.devices.lasers.base.LaserBase method) (navigate.model.devices.lasers.synthetic.SyntheticLaser method) turn_on_laser() (navigate.model.microscope.Microscope method)

U

unload_sample() (navigate.model.devices.stages.synthetic.SyntheticStage method) unlock() (navigate.controller.thread_pool.SelfLockThread method) unreceived_bytes (navigate.model.devices.APIs.sutter.MP285.MP285 attribute) update_analog_task() (navigate.model.devices.daq.synthetic.SyntheticDAQ method) update_channel() (navigate.model.features.common_features.ZStackAcquisition method) update_config_dict() (in module navigate.config.config) update_data_buffer() (navigate.model.microscope.Microscope method) (navigate.model.model.Model method)

update_ilastik_setting() (navigate.model.model.Model method) update_mirror() (navigate.model.model.Model method) update_nested_dict() (in module navigate.tools.common_dict_tools) update_setting() (navigate.model.features.restful_features.IlastikSegmentation method) update_stage_dict() (in module navigate.tools.common_dict_tools) update_stage_limits() (navigate.model.microscope.Microscope method) update_table() (in module navigate.tools.multipos_table_tools) UPDATEIFCOPY (navigate.model.concurrency.concurrency_tools.SharedNDArray attribute)

V

var() (navigate.model.concurrency.concurrency_tools.SharedNDArray method) VariableWithLock (class in navigate.tools.common_functions) variance (navigate.model.devices.camera.base.CameraBase property) (navigate.model.devices.camera.hamamatsu.HamamatsuBase property) (navigate.model.devices.camera.hamamatsu.HamamatsuOrca property) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaFire property) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaFusion property) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaLightning property) (navigate.model.devices.camera.synthetic.SyntheticCamera property) verbose (navigate.model.devices.APIs.asi.asi_MFC_controller.MFCTwoThousand attribute) (navigate.model.devices.APIs.asi.asi_MS2000_controller.MS2000Controller attribute) (navigate.model.devices.APIs.asi.asi_tiger_controller.TigerController attribute) verify_abs_position() (navigate.model.devices.stages.asi.ASIStage method) (navigate.model.devices.stages.asi_MSTwoThousand.ASIStage method) (navigate.model.devices.stages.base.StageBase method) (navigate.model.devices.stages.mcl.MCLStage method) (navigate.model.devices.stages.pi.PIStage method) (navigate.model.devices.stages.sutter.SutterStage method) (navigate.model.devices.stages.synthetic.SyntheticStage method) (navigate.model.devices.stages.tl_kcube_inertial.TLKIMStage method) (navigate.model.devices.stages.tl_kcube_steppermotor.TLKSTStage method)

verify_configuration() (in module navigate.config.config) verify_experiment_config() (in module navigate.config.config) verify_move() (navigate.model.devices.stages.asi.ASIStage method) (navigate.model.devices.stages.asi_MSTwoThousand.ASIStage method) verify_positions_config() (in module navigate.config.config) verify_waveform_constants() (in module navigate.config.config) view() (navigate.model.concurrency.concurrency_tools.SharedNDArray method) virtual_microscopes (navigate.model.model.Model attribute) volume_from_sdf() (in module navigate.tools.sdf) volumes_selected (navigate.model.features.volume_search.VolumeSearch attribute) VolumeSearch (class in navigate.model.features.volume_search) voxel_size (navigate.model.data_sources.bdv_data_source.BigDataViewerDataSource property) (navigate.model.data_sources.data_source.DataSource property) (navigate.model.data_sources.pyramidal_data_source.PyramidalDataSource property) (navigate.model.data_sources.tiff_data_source.TiffDataSource property) (navigate.model.data_sources.zarr_data_source.OMEZarrDataSource property) (navigate.model.metadata_sources.bdv_metadata.BigDataViewerMetadata property) (navigate.model.metadata_sources.metadata.Metadata property) (navigate.model.metadata_sources.metadata.XMLMetadata property) (navigate.model.metadata_sources.ome_tiff_metadata.OMETIFFMetadata property) (navigate.model.metadata_sources.zarr_metadata.OMEZarrMetadata property)

W

wait() (navigate.controller.thread_pool.SelfLockThread method) wait_for_device() (navigate.model.devices.APIs.asi.asi_MFC_controller.MFCTwoThousand method) (navigate.model.devices.APIs.asi.asi_MS2000_controller.MS2000Controller method) (navigate.model.devices.APIs.asi.asi_tiger_controller.TigerController method) wait_on_target() (navigate.model.devices.stages.pi.PIStage method) wait_time (navigate.model.devices.APIs.sutter.MP285.MP285 attribute) wait_to_run_lock (navigate.model.devices.daq.synthetic.SyntheticDAQ attribute) wait_until_done (navigate.model.devices.APIs.sutter.MP285.MP285 attribute) (navigate.model.devices.filter_wheel.sutter.SutterFilterWheel attribute) wait_until_done_delay (navigate.model.devices.filter_wheel.asi.ASICubeSlider attribute) (navigate.model.devices.filter_wheel.asi.ASIFilterWheel attribute) (navigate.model.devices.filter_wheel.ludl.LUDLFilterWheel attribute) (navigate.model.devices.filter_wheel.sutter.SutterFilterWheel attribute) WaitForExternalTrigger (class in navigate.model.features.common_features) waitlist (navigate.controller.thread_pool.ThreadWaitlist attribute) waitlistLock (navigate.controller.thread_pool.ThreadWaitlist attribute) WaitToContinue (class in navigate.model.features.common_features) waveform_constants (navigate.model.devices.daq.base.DAQBase attribute) (navigate.model.devices.daq.synthetic.SyntheticDAQ attribute) waveform_dict (navigate.model.devices.daq.base.DAQBase attribute) (navigate.model.devices.daq.synthetic.SyntheticDAQ attribute) (navigate.model.devices.galvo.base.GalvoBase attribute) (navigate.model.devices.galvo.synthetic.SyntheticGalvo attribute) (navigate.model.devices.remote_focus.base.RemoteFocusBase attribute) (navigate.model.devices.remote_focus.equipment_solutions.RemoteFocusEquipmentSolutions attribute) (navigate.model.devices.remote_focus.ni.RemoteFocusNI attribute) (navigate.model.devices.remote_focus.synthetic.SyntheticRemoteFocus attribute)

waveform_expand_num (navigate.model.devices.daq.base.DAQBase attribute) (navigate.model.devices.daq.synthetic.SyntheticDAQ attribute) waveform_repeat_num (navigate.model.devices.daq.base.DAQBase attribute) (navigate.model.devices.daq.synthetic.SyntheticDAQ attribute) wheel_position (navigate.model.devices.filter_wheel.asi.ASICubeSlider attribute) (navigate.model.devices.filter_wheel.asi.ASIFilterWheel attribute) (navigate.model.devices.filter_wheel.base.FilterWheelBase attribute) (navigate.model.devices.filter_wheel.ludl.LUDLFilterWheel attribute) (navigate.model.devices.filter_wheel.sutter.SutterFilterWheel attribute) (navigate.model.devices.filter_wheel.synthetic.SyntheticFilterWheel attribute) write() (navigate.model.data_sources.bdv_data_source.BigDataViewerDataSource method) (navigate.model.data_sources.data_source.DataSource method) (navigate.model.data_sources.pyramidal_data_source.PyramidalDataSource method) (navigate.model.data_sources.tiff_data_source.TiffDataSource method) (navigate.model.data_sources.zarr_data_source.OMEZarrDataSource method) (navigate.model.devices.APIs.omicron.LuxxLaser.LuxxLaser method) write_done_flag (navigate.model.devices.APIs.sutter.MP285.MP285 attribute) write_waveforms_to_tasks() (navigate.model.devices.daq.synthetic.SyntheticDAQ method) write_xml() (navigate.model.metadata_sources.bdv_metadata.BigDataViewerMetadata method) (navigate.model.metadata_sources.metadata.XMLMetadata method) (navigate.model.metadata_sources.ome_tiff_metadata.OMETIFFMetadata method) WRITEABLE (navigate.model.concurrency.concurrency_tools.SharedNDArray attribute) WRITEBACKIFCOPY (navigate.model.concurrency.concurrency_tools.SharedNDArray attribute)

X

x_binning (navigate.model.devices.camera.synthetic.SyntheticCamera attribute) x_pixels (navigate.model.devices.camera.base.CameraBase attribute) (navigate.model.devices.camera.hamamatsu.HamamatsuBase attribute) (navigate.model.devices.camera.hamamatsu.HamamatsuOrca attribute) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaFire attribute) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaFusion attribute) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaLightning attribute) (navigate.model.devices.camera.synthetic.SyntheticCamera attribute)

XMLMetadata (class in navigate.model.metadata_sources.metadata)

Y

y_binning (navigate.model.devices.camera.synthetic.SyntheticCamera attribute) y_pixels (navigate.model.devices.camera.base.CameraBase attribute) (navigate.model.devices.camera.hamamatsu.HamamatsuBase attribute) (navigate.model.devices.camera.hamamatsu.HamamatsuOrca attribute) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaFire attribute) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaFusion attribute) (navigate.model.devices.camera.hamamatsu.HamamatsuOrcaLightning attribute) (navigate.model.devices.camera.synthetic.SyntheticCamera attribute)

Z

z_pos (navigate.model.features.volume_search.VolumeSearch attribute) z_position_moved_time (navigate.model.features.common_features.ZStackAcquisition attribute) z_step_size (navigate.model.features.common_features.ZStackAcquisition attribute) (navigate.model.features.volume_search.VolumeSearch attribute) z_steps (navigate.model.features.volume_search.VolumeSearch attribute) zero_flatness() (navigate.model.devices.mirrors.imop.ImagineOpticsMirror method) zoom (navigate.model.features.restful_features.IlastikSegmentation attribute) zoom_value (navigate.model.features.common_features.ChangeResolution attribute) (navigate.model.features.common_features.MoveToNextPositionInMultiPositionTable attribute)

ZoomBase (class in navigate.model.devices.zoom.base) zoomdict (navigate.model.devices.zoom.base.ZoomBase attribute) (navigate.model.devices.zoom.dynamixel.DynamixelZoom attribute) (navigate.model.devices.zoom.synthetic.SyntheticZoom attribute) zoomvalue (navigate.model.devices.zoom.base.ZoomBase attribute) (navigate.model.devices.zoom.dynamixel.DynamixelZoom attribute) (navigate.model.devices.zoom.synthetic.SyntheticZoom attribute) ZStackAcquisition (class in navigate.model.features.common_features)