navigate
Getting Started
Quick Start Guide
Software Installation
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User Guide
Supported Hardware
Supported File Formats
User Interface Walkthrough
Setting Up A Microscope
Acquiring Data
Case Studies
Development
Software Architecture
Contributing Guidelines
Feature Container
REST-API
Plugin Architecture
Plugins
navigate Plugin Template
navigate Confocal Projection Plugin
navigate at Scale
navigate MMCore Plugin
navigate ilastik Server
Reference
Implemented Microscopes
Software API
navigate
Index
Index
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A
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B
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C
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D
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E
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F
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G
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H
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I
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J
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K
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L
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M
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N
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O
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P
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R
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S
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T
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U
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V
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W
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X
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Y
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Z
_
__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.camera_base.CameraBase method)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuBase method)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrca method)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaFire method)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaFusion method)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaLightning method)
(navigate.model.devices.camera.camera_synthetic.SyntheticCamera method)
(navigate.model.devices.camera.camera_synthetic.SyntheticCameraController method)
(navigate.model.devices.daq.daq_base.DAQBase method)
(navigate.model.devices.daq.daq_synthetic.SyntheticDAQ method)
(navigate.model.devices.filter_wheel.filter_wheel_asi.ASIFilterWheel method)
(navigate.model.devices.filter_wheel.filter_wheel_base.FilterWheelBase method)
(navigate.model.devices.filter_wheel.filter_wheel_ludl.LUDLFilterWheel method)
(navigate.model.devices.filter_wheel.filter_wheel_sutter.SutterFilterWheel method)
(navigate.model.devices.filter_wheel.filter_wheel_synthetic.SyntheticFilterWheel method)
(navigate.model.devices.galvo.galvo_base.GalvoBase method)
(navigate.model.devices.galvo.galvo_synthetic.SyntheticGalvo method)
(navigate.model.devices.lasers.laser_base.LaserBase method)
(navigate.model.devices.lasers.laser_synthetic.SyntheticLaser method)
(navigate.model.devices.mirrors.mirror_base.MirrorBase method)
(navigate.model.devices.mirrors.mirror_imop.ImagineOpticsMirror method)
(navigate.model.devices.mirrors.mirror_synthetic.SyntheticMirror method)
(navigate.model.devices.objectives.Objective method)
(navigate.model.devices.remote_focus.remote_focus_base.RemoteFocusBase method)
(navigate.model.devices.remote_focus.remote_focus_synthetic.SyntheticRemoteFocus method)
(navigate.model.devices.shutter.laser_shutter_base.ShutterBase method)
(navigate.model.devices.shutter.laser_shutter_synthetic.SyntheticShutter method)
(navigate.model.devices.stages.stage_asi.ASIStage method)
(navigate.model.devices.stages.stage_asi_MSTwoThousand.ASIStage method)
(navigate.model.devices.stages.stage_base.StageBase method)
(navigate.model.devices.stages.stage_mcl.MCLStage method)
(navigate.model.devices.stages.stage_pi.PIStage method)
(navigate.model.devices.stages.stage_sutter.SutterStage method)
(navigate.model.devices.stages.stage_synthetic.SyntheticStage method)
(navigate.model.devices.stages.stage_tl_kcube_inertial.TLKIMStage method)
(navigate.model.devices.stages.stage_tl_kcube_steppermotor.TLKSTStage method)
(navigate.model.devices.zoom.zoom_base.ZoomBase method)
(navigate.model.devices.zoom.zoom_dynamixel.DynamixelZoom method)
(navigate.model.devices.zoom.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.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.cva_conpro.ConstantVelocityAcquisition 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.daq_synthetic.SyntheticDAQ method)
addon_feature (navigate.model.model.Model attribute)
addr_mx_goal_position (navigate.model.devices.zoom.zoom_dynamixel.DynamixelZoom attribute)
addr_mx_moving_speed (navigate.model.devices.zoom.zoom_dynamixel.DynamixelZoom attribute)
addr_mx_p_gain (navigate.model.devices.zoom.zoom_dynamixel.DynamixelZoom attribute)
addr_mx_present_position (navigate.model.devices.zoom.zoom_dynamixel.DynamixelZoom attribute)
addr_mx_torque_enable (navigate.model.devices.zoom.zoom_dynamixel.DynamixelZoom attribute)
addr_mx_torque_limit (navigate.model.devices.zoom.zoom_dynamixel.DynamixelZoom attribute)
adjust() (navigate.model.devices.galvo.galvo_base.GalvoBase method)
(navigate.model.devices.galvo.galvo_synthetic.SyntheticGalvo method)
(navigate.model.devices.remote_focus.remote_focus_base.RemoteFocusBase method)
(navigate.model.devices.remote_focus.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.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.stage_asi_MSTwoThousand.ASIStage attribute)
ASIFilterWheel (class in navigate.model.devices.filter_wheel.filter_wheel_asi)
ASIStage (class in navigate.model.devices.stages.stage_asi)
(class in navigate.model.devices.stages.stage_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.stage_asi.ASIStage attribute)
(navigate.model.devices.stages.stage_asi_MSTwoThousand.ASIStage attribute)
(navigate.model.devices.stages.stage_base.StageBase attribute)
(navigate.model.devices.stages.stage_mcl.MCLStage attribute)
(navigate.model.devices.stages.stage_pi.PIStage attribute)
(navigate.model.devices.stages.stage_sutter.SutterStage attribute)
(navigate.model.devices.stages.stage_synthetic.SyntheticStage attribute)
(navigate.model.devices.stages.stage_tl_kcube_inertial.TLKIMStage attribute)
(navigate.model.devices.stages.stage_tl_kcube_steppermotor.TLKSTStage attribute)
axes_mapping (navigate.model.devices.stages.stage_asi.ASIStage attribute)
(navigate.model.devices.stages.stage_asi_MSTwoThousand.ASIStage attribute)
(navigate.model.devices.stages.stage_base.StageBase attribute)
(navigate.model.devices.stages.stage_mcl.MCLStage attribute)
(navigate.model.devices.stages.stage_pi.PIStage attribute)
(navigate.model.devices.stages.stage_sutter.SutterStage attribute)
(navigate.model.devices.stages.stage_synthetic.SyntheticStage attribute)
(navigate.model.devices.stages.stage_tl_kcube_inertial.TLKIMStage attribute)
(navigate.model.devices.stages.stage_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)
baudrate (in module navigate.model.devices.filter_wheel.filter_wheel_ludl)
(in module navigate.model.devices.filter_wheel.filter_wheel_sutter)
(navigate.model.devices.filter_wheel.filter_wheel_synthetic.SyntheticFilterWheel attribute)
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)
box() (in module navigate.tools.sdf)
build_ASI_Stage_connection() (in module navigate.model.devices.stages.stage_asi)
(in module navigate.model.devices.stages.stage_asi_MFCTwoThousand)
(in module navigate.model.devices.stages.stage_asi_MSTwoThousand)
build_dynamixel_zoom_connection() (in module navigate.model.devices.zoom.zoom_dynamixel)
build_filter_wheel_connection() (in module navigate.model.devices.filter_wheel.filter_wheel_asi)
(in module navigate.model.devices.filter_wheel.filter_wheel_ludl)
(in module navigate.model.devices.filter_wheel.filter_wheel_sutter)
build_MCLStage_connection() (in module navigate.model.devices.stages.stage_mcl)
build_MP285_connection() (in module navigate.model.devices.stages.stage_sutter)
build_nested_dict() (in module navigate.config.config)
build_PIStage_connection() (in module navigate.model.devices.stages.stage_pi)
build_ref_name() (in module navigate.tools.common_functions)
build_stage_dict() (navigate.model.devices.zoom.zoom_base.ZoomBase method)
(navigate.model.devices.zoom.zoom_dynamixel.DynamixelZoom method)
(navigate.model.devices.zoom.zoom_synthetic.SyntheticZoom method)
build_TLKIMStage_connection() (in module navigate.model.devices.stages.stage_tl_kcube_inertial)
build_TLKSTStage_connection() (in module navigate.model.devices.stages.stage_tl_kcube_steppermotor)
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.daq_base.DAQBase method)
(navigate.model.devices.daq.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.camera_base.CameraBase method)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuBase method)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrca method)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaFire method)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaFusion method)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaLightning method)
(navigate.model.devices.camera.camera_synthetic.SyntheticCamera method)
calculate_readout_time() (navigate.model.devices.camera.camera_hamamatsu.HamamatsuBase method)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrca method)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaFire method)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaFusion method)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaLightning method)
(navigate.model.devices.camera.camera_synthetic.SyntheticCamera method)
CalculateFocusRange (class in navigate.model.features.auto_tile_scan)
camera (navigate.model.devices.daq.daq_synthetic.SyntheticDAQ attribute)
camera_config_dict (navigate.controller.configuration_controller.ConfigurationController property)
camera_controller (navigate.model.devices.camera.camera_base.CameraBase attribute)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuBase attribute)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrca attribute)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaFire attribute)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaFusion attribute)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaLightning attribute)
(navigate.model.devices.camera.camera_synthetic.SyntheticCamera attribute)
camera_delay (navigate.model.devices.daq.daq_base.DAQBase attribute)
(navigate.model.devices.daq.daq_synthetic.SyntheticDAQ attribute)
(navigate.model.devices.galvo.galvo_base.GalvoBase attribute)
(navigate.model.devices.galvo.galvo_synthetic.SyntheticGalvo attribute)
(navigate.model.devices.remote_focus.remote_focus_base.RemoteFocusBase attribute)
(navigate.model.devices.remote_focus.remote_focus_synthetic.SyntheticRemoteFocus attribute)
camera_exposure() (in module navigate.model.waveforms)
camera_exposure_time (navigate.model.devices.camera.camera_synthetic.SyntheticCamera attribute)
camera_flip_flags (navigate.controller.configuration_controller.ConfigurationController property)
camera_parameters (navigate.model.devices.camera.camera_base.CameraBase attribute)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuBase attribute)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrca attribute)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaFire attribute)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaFusion attribute)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaLightning attribute)
(navigate.model.devices.camera.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.camera_base)
CARRAY (navigate.model.concurrency.concurrency_tools.SharedNDArray 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.filter_wheel_asi.ASIFilterWheel method)
(navigate.model.devices.filter_wheel.filter_wheel_base.FilterWheelBase method)
(navigate.model.devices.filter_wheel.filter_wheel_ludl.LUDLFilterWheel method)
(navigate.model.devices.filter_wheel.filter_wheel_sutter.SutterFilterWheel method)
(navigate.model.devices.filter_wheel.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.cva_conpro.ConstantVelocityAcquisition 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)
cleanup_data_function() (navigate.model.features.cva_conpro.ConstantVelocityAcquisition 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.filter_wheel_asi.ASIFilterWheel method)
(navigate.model.devices.filter_wheel.filter_wheel_ludl.LUDLFilterWheel method)
(navigate.model.devices.filter_wheel.filter_wheel_sutter.SutterFilterWheel method)
(navigate.model.devices.filter_wheel.filter_wheel_synthetic.SyntheticFilterWheel method)
(navigate.model.devices.lasers.laser_base.LaserBase method)
(navigate.model.devices.lasers.laser_synthetic.SyntheticLaser method)
(navigate.model.devices.stages.stage_asi.ASIStage method)
(navigate.model.devices.stages.stage_asi_MSTwoThousand.ASIStage method)
(navigate.model.devices.stages.stage_base.StageBase method)
(navigate.model.devices.stages.stage_mcl.MCLStage method)
(navigate.model.devices.stages.stage_pi.PIStage method)
(navigate.model.devices.stages.stage_sutter.SutterStage method)
(navigate.model.devices.stages.stage_synthetic.SyntheticStage method)
(navigate.model.devices.stages.stage_tl_kcube_inertial.TLKIMStage method)
(navigate.model.devices.stages.stage_tl_kcube_steppermotor.TLKSTStage method)
(navigate.model.features.image_writer.ImageWriter method)
close_camera() (navigate.model.devices.camera.camera_base.CameraBase method)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuBase method)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrca method)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaFire method)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaFusion method)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaLightning method)
(navigate.model.devices.camera.camera_synthetic.SyntheticCamera method)
close_image_series() (navigate.model.devices.camera.camera_hamamatsu.HamamatsuBase method)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrca method)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaFire method)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaFusion method)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaLightning method)
(navigate.model.devices.camera.camera_synthetic.SyntheticCamera method)
close_shutter() (navigate.model.devices.shutter.laser_shutter_base.ShutterBase method)
(navigate.model.devices.shutter.laser_shutter_synthetic.SyntheticShutter method)
close_tasks() (navigate.model.devices.daq.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)
comport (in module navigate.model.devices.filter_wheel.filter_wheel_ludl)
(in module navigate.model.devices.filter_wheel.filter_wheel_sutter)
(navigate.model.devices.filter_wheel.filter_wheel_synthetic.SyntheticFilterWheel 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.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.camera_base.CameraBase attribute)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuBase attribute)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrca attribute)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaFire attribute)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaFusion attribute)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaLightning attribute)
(navigate.model.devices.camera.camera_synthetic.SyntheticCamera attribute)
(navigate.model.devices.daq.daq_base.DAQBase attribute)
(navigate.model.devices.daq.daq_synthetic.SyntheticDAQ attribute)
(navigate.model.devices.galvo.galvo_base.GalvoBase attribute)
(navigate.model.devices.galvo.galvo_synthetic.SyntheticGalvo attribute)
(navigate.model.devices.lasers.laser_base.LaserBase attribute)
(navigate.model.devices.lasers.laser_synthetic.SyntheticLaser attribute)
(navigate.model.devices.mirrors.mirror_base.MirrorBase attribute)
(navigate.model.devices.mirrors.mirror_imop.ImagineOpticsMirror attribute)
(navigate.model.devices.mirrors.mirror_synthetic.SyntheticMirror attribute)
(navigate.model.devices.remote_focus.remote_focus_base.RemoteFocusBase attribute)
(navigate.model.devices.remote_focus.remote_focus_synthetic.SyntheticRemoteFocus attribute)
(navigate.model.devices.zoom.zoom_base.ZoomBase attribute)
(navigate.model.devices.zoom.zoom_dynamixel.DynamixelZoom attribute)
(navigate.model.devices.zoom.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)
ConstantVelocityAcquisition (class in navigate.model.features.cva_conpro)
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.daq_synthetic.SyntheticDAQ method)
create_galvo_remote_focus_tasks() (navigate.model.devices.daq.daq_synthetic.SyntheticDAQ method)
create_master_trigger_task() (navigate.model.devices.daq.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.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_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.microscope.Microscope attribute)
daq_parameters (navigate.model.devices.daq.daq_base.DAQBase attribute)
(navigate.model.devices.daq.daq_synthetic.SyntheticDAQ attribute)
daq_sample_rate (navigate.controller.configuration_controller.ConfigurationController property)
DAQBase (class in navigate.model.devices.daq.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.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.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.stage_synthetic.SyntheticStage attribute)
defocus (navigate.model.features.common_features.ZStackAcquisition attribute)
delay_matrix (navigate.model.devices.filter_wheel.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.stage_sutter.SutterStage attribute)
device_config (navigate.model.devices.APIs.coherent.ObisLaser.ObisLaser attribute)
(navigate.model.devices.APIs.omicron.LuxxLaser.LuxxLaser attribute)
(navigate.model.devices.galvo.galvo_base.GalvoBase attribute)
(navigate.model.devices.galvo.galvo_synthetic.SyntheticGalvo attribute)
(navigate.model.devices.lasers.laser_base.LaserBase attribute)
(navigate.model.devices.lasers.laser_synthetic.SyntheticLaser attribute)
(navigate.model.devices.remote_focus.remote_focus_base.RemoteFocusBase attribute)
(navigate.model.devices.remote_focus.remote_focus_synthetic.SyntheticRemoteFocus 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.stage_tl_kcube_steppermotor.TLKSTStage attribute)
diagonal() (navigate.model.concurrency.concurrency_tools.SharedNDArray method)
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)
display_modes() (navigate.model.devices.mirrors.mirror_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.zoom_dynamixel.DynamixelZoom attribute)
DynamixelZoom (class in navigate.model.devices.zoom.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.daq_base.DAQBase method)
(navigate.model.devices.daq.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)
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.daq_base.DAQBase attribute)
(navigate.model.devices.daq.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)
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.filter_wheel_asi.ASIFilterWheel method)
(navigate.model.devices.filter_wheel.filter_wheel_sutter.SutterFilterWheel method)
(navigate.model.devices.filter_wheel.filter_wheel_synthetic.SyntheticFilterWheel method)
filter_dictionary (navigate.model.devices.filter_wheel.filter_wheel_asi.ASIFilterWheel attribute)
(navigate.model.devices.filter_wheel.filter_wheel_base.FilterWheelBase attribute)
(navigate.model.devices.filter_wheel.filter_wheel_ludl.LUDLFilterWheel attribute)
(navigate.model.devices.filter_wheel.filter_wheel_sutter.SutterFilterWheel attribute)
(navigate.model.devices.filter_wheel.filter_wheel_synthetic.SyntheticFilterWheel attribute)
,
[1]
filter_wheel (navigate.model.devices.filter_wheel.filter_wheel_asi.ASIFilterWheel attribute)
(navigate.model.microscope.Microscope attribute)
filter_wheel_number (navigate.model.devices.filter_wheel.filter_wheel_asi.ASIFilterWheel attribute)
(navigate.model.devices.filter_wheel.filter_wheel_base.FilterWheelBase attribute)
(navigate.model.devices.filter_wheel.filter_wheel_ludl.LUDLFilterWheel attribute)
(navigate.model.devices.filter_wheel.filter_wheel_sutter.SutterFilterWheel attribute)
(navigate.model.devices.filter_wheel.filter_wheel_synthetic.SyntheticFilterWheel attribute)
filter_wheel_position (navigate.model.devices.filter_wheel.filter_wheel_asi.ASIFilterWheel attribute)
filter_wheel_setting_dict (navigate.controller.configuration_controller.ConfigurationController property)
FilterWheelBase (class in navigate.model.devices.filter_wheel.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.mirror_imop.ImagineOpticsMirror method)
(navigate.model.devices.mirrors.mirror_synthetic.SyntheticMirror method)
flatten() (navigate.model.concurrency.concurrency_tools.SharedNDArray method)
flush_buffers() (navigate.model.devices.APIs.sutter.MP285.MP285 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_max_voltage (navigate.model.devices.galvo.galvo_base.GalvoBase attribute)
(navigate.model.devices.galvo.galvo_synthetic.SyntheticGalvo attribute)
galvo_min_voltage (navigate.model.devices.galvo.galvo_base.GalvoBase attribute)
(navigate.model.devices.galvo.galvo_synthetic.SyntheticGalvo attribute)
galvo_name (navigate.model.devices.galvo.galvo_base.GalvoBase attribute)
(navigate.model.devices.galvo.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.galvo_base.GalvoBase attribute)
(navigate.model.devices.galvo.galvo_synthetic.SyntheticGalvo attribute)
GalvoBase (class in navigate.model.devices.galvo.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.camera_synthetic.SyntheticCamera method)
get_abs_position() (navigate.model.devices.stages.stage_asi.ASIStage method)
(navigate.model.devices.stages.stage_asi_MSTwoThousand.ASIStage method)
(navigate.model.devices.stages.stage_base.StageBase method)
(navigate.model.devices.stages.stage_mcl.MCLStage method)
(navigate.model.devices.stages.stage_pi.PIStage method)
(navigate.model.devices.stages.stage_sutter.SutterStage method)
(navigate.model.devices.stages.stage_synthetic.SyntheticStage method)
(navigate.model.devices.stages.stage_tl_kcube_inertial.TLKIMStage method)
(navigate.model.devices.stages.stage_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_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.stage_asi.ASIStage method)
(navigate.model.devices.stages.stage_asi_MSTwoThousand.ASIStage method)
(navigate.model.devices.stages.stage_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.camera_base.CameraBase method)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuBase method)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrca method)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaFire method)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaFusion method)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaLightning method)
(navigate.model.devices.camera.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.mirror_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.camera_hamamatsu.HamamatsuBase method)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrca method)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaFire method)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaFusion method)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaLightning method)
(navigate.model.devices.camera.camera_synthetic.SyntheticCamera method)
get_offset_variance_maps() (navigate.model.devices.camera.camera_base.CameraBase method)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuBase method)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrca method)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaFire method)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaFusion method)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaLightning method)
(navigate.model.devices.camera.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.stage_asi.ASIStage method)
(navigate.model.devices.stages.stage_asi_MSTwoThousand.ASIStage method)
(navigate.model.devices.stages.stage_base.StageBase method)
(navigate.model.devices.stages.stage_mcl.MCLStage method)
(navigate.model.devices.stages.stage_pi.PIStage method)
(navigate.model.devices.stages.stage_sutter.SutterStage method)
(navigate.model.devices.stages.stage_synthetic.SyntheticStage method)
(navigate.model.devices.stages.stage_tl_kcube_inertial.TLKIMStage method)
(navigate.model.devices.stages.stage_tl_kcube_steppermotor.TLKSTStage method)
get_power() (navigate.model.devices.APIs.omicron.LuxxLaser.LuxxLaser method)
get_property_value() (navigate.model.devices.camera.camera_synthetic.SyntheticCameraController method)
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.stage_asi.ASIStage method)
(navigate.model.devices.stages.stage_asi_MSTwoThousand.ASIStage method)
(navigate.model.devices.stages.stage_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)
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.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.camera_hamamatsu)
HamamatsuOrca (class in navigate.model.devices.camera.camera_hamamatsu)
HamamatsuOrcaFire (class in navigate.model.devices.camera.camera_hamamatsu)
HamamatsuOrcaFusion (class in navigate.model.devices.camera.camera_hamamatsu)
HamamatsuOrcaLightning (class in navigate.model.devices.camera.camera_hamamatsu)
handle (navigate.model.devices.stages.stage_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.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.mirror_imop)
imaging_mode (navigate.model.model.Model attribute)
img_height (navigate.model.model.Model 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.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.camera_hamamatsu.HamamatsuBase method)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrca method)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaFire method)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaFusion method)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaLightning method)
(navigate.model.devices.camera.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.laser_base.LaserBase method)
(navigate.model.devices.lasers.laser_synthetic.SyntheticLaser method)
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.camera_base.CameraBase attribute)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuBase attribute)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrca attribute)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaFire attribute)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaFusion attribute)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaLightning attribute)
(navigate.model.devices.camera.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_live (navigate.model.model.Model attribute)
is_marked (navigate.model.features.feature_container.DataNode 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.mirror_base.MirrorBase attribute)
(navigate.model.devices.mirrors.mirror_imop.ImagineOpticsMirror attribute)
(navigate.model.devices.mirrors.mirror_synthetic.SyntheticMirror attribute)
(navigate.model.microscope.Microscope attribute)
is_updating_analog_task (navigate.model.devices.daq.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.stage_tl_kcube_inertial.TLKIMStage attribute)
kim_controller (navigate.model.devices.stages.stage_tl_kcube_inertial.TLKIMStage attribute)
KST_axes (navigate.model.devices.stages.stage_tl_kcube_steppermotor.TLKSTStage attribute)
kst_controller (navigate.model.devices.stages.stage_tl_kcube_steppermotor.TLKSTStage attribute)
L
laser_wavelength (navigate.model.microscope.Microscope attribute)
LaserBase (class in navigate.model.devices.lasers.laser_base)
lasers (navigate.model.microscope.Microscope attribute)
lasers_info (navigate.controller.configuration_controller.ConfigurationController property)
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.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_sample() (navigate.model.devices.stages.stage_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_setup() (in module navigate.log_files.log_functions)
logger (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.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.stage_mcl.MCLStage attribute)
MCLStage (class in navigate.model.devices.stages.stage_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.daq.daq_base.DAQBase attribute)
(navigate.model.devices.daq.daq_synthetic.SyntheticDAQ attribute)
(navigate.model.devices.galvo.galvo_base.GalvoBase attribute)
(navigate.model.devices.galvo.galvo_synthetic.SyntheticGalvo attribute)
(navigate.model.devices.lasers.laser_base.LaserBase attribute)
(navigate.model.devices.lasers.laser_synthetic.SyntheticLaser attribute)
(navigate.model.devices.remote_focus.remote_focus_base.RemoteFocusBase attribute)
(navigate.model.devices.remote_focus.remote_focus_synthetic.SyntheticRemoteFocus 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.camera_base.CameraBase attribute)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuBase attribute)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrca attribute)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaFire attribute)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaFusion attribute)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaLightning attribute)
(navigate.model.devices.camera.camera_synthetic.SyntheticCamera attribute)
min_image_width (navigate.model.devices.camera.camera_base.CameraBase attribute)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuBase attribute)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrca attribute)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaFire attribute)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaFusion attribute)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaLightning attribute)
(navigate.model.devices.camera.camera_synthetic.SyntheticCamera attribute)
minimum_exposure_time (navigate.model.devices.camera.camera_base.CameraBase attribute)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuBase attribute)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrca attribute)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaFire attribute)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaFusion attribute)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaLightning attribute)
(navigate.model.devices.camera.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.mirror_base.MirrorBase attribute)
(navigate.model.devices.mirrors.mirror_imop.ImagineOpticsMirror attribute)
(navigate.model.devices.mirrors.mirror_synthetic.SyntheticMirror attribute)
(navigate.model.features.adaptive_optics.TonyWilson attribute)
mirror_parameters (navigate.model.devices.mirrors.mirror_base.MirrorBase attribute)
(navigate.model.devices.mirrors.mirror_imop.ImagineOpticsMirror attribute)
(navigate.model.devices.mirrors.mirror_synthetic.SyntheticMirror attribute)
MirrorBase (class in navigate.model.devices.mirrors.mirror_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.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.camera_base
navigate.model.devices.camera.camera_hamamatsu
navigate.model.devices.camera.camera_synthetic
navigate.model.devices.daq
navigate.model.devices.daq.daq_base
navigate.model.devices.daq.daq_synthetic
navigate.model.devices.filter_wheel
navigate.model.devices.filter_wheel.filter_wheel_asi
navigate.model.devices.filter_wheel.filter_wheel_base
navigate.model.devices.filter_wheel.filter_wheel_ludl
navigate.model.devices.filter_wheel.filter_wheel_sutter
navigate.model.devices.filter_wheel.filter_wheel_synthetic
navigate.model.devices.galvo
navigate.model.devices.galvo.galvo_base
navigate.model.devices.galvo.galvo_synthetic
navigate.model.devices.lasers
navigate.model.devices.lasers.laser_base
navigate.model.devices.lasers.laser_synthetic
navigate.model.devices.mirrors
navigate.model.devices.mirrors.mirror_base
navigate.model.devices.mirrors.mirror_imop
navigate.model.devices.mirrors.mirror_synthetic
navigate.model.devices.objectives
navigate.model.devices.remote_focus
navigate.model.devices.remote_focus.remote_focus_base
navigate.model.devices.remote_focus.remote_focus_synthetic
navigate.model.devices.shutter
navigate.model.devices.shutter.laser_shutter_base
navigate.model.devices.shutter.laser_shutter_synthetic
navigate.model.devices.stages
navigate.model.devices.stages.stage_asi
navigate.model.devices.stages.stage_asi_MFCTwoThousand
navigate.model.devices.stages.stage_asi_MSTwoThousand
navigate.model.devices.stages.stage_base
navigate.model.devices.stages.stage_mcl
navigate.model.devices.stages.stage_pi
navigate.model.devices.stages.stage_sutter
navigate.model.devices.stages.stage_synthetic
navigate.model.devices.stages.stage_tl_kcube_inertial
navigate.model.devices.stages.stage_tl_kcube_steppermotor
navigate.model.devices.zoom
navigate.model.devices.zoom.zoom_base
navigate.model.devices.zoom.zoom_dynamixel
navigate.model.devices.zoom.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.cva_conpro
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.remote_focus_synthetic.SyntheticRemoteFocus method)
(navigate.model.devices.zoom.zoom_base.ZoomBase method)
(navigate.model.devices.zoom.zoom_dynamixel.DynamixelZoom method)
(navigate.model.devices.zoom.zoom_synthetic.SyntheticZoom method)
move_absolute() (navigate.model.devices.stages.stage_asi.ASIStage method)
(navigate.model.devices.stages.stage_asi_MSTwoThousand.ASIStage method)
(navigate.model.devices.stages.stage_mcl.MCLStage method)
(navigate.model.devices.stages.stage_pi.PIStage method)
(navigate.model.devices.stages.stage_sutter.SutterStage method)
(navigate.model.devices.stages.stage_synthetic.SyntheticStage method)
(navigate.model.devices.stages.stage_tl_kcube_inertial.TLKIMStage method)
(navigate.model.devices.stages.stage_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.stage_asi.ASIStage method)
(navigate.model.devices.stages.stage_asi_MSTwoThousand.ASIStage method)
(navigate.model.devices.stages.stage_mcl.MCLStage method)
(navigate.model.devices.stages.stage_pi.PIStage method)
(navigate.model.devices.stages.stage_sutter.SutterStage method)
(navigate.model.devices.stages.stage_synthetic.SyntheticStage method)
(navigate.model.devices.stages.stage_tl_kcube_inertial.TLKIMStage method)
(navigate.model.devices.stages.stage_tl_kcube_steppermotor.TLKSTStage method)
move_axis_relative() (navigate.model.devices.stages.stage_asi_MSTwoThousand.ASIStage 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.stage_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.stage_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)
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.camera_base
module
navigate.model.devices.camera.camera_hamamatsu
module
navigate.model.devices.camera.camera_synthetic
module
navigate.model.devices.daq
module
navigate.model.devices.daq.daq_base
module
navigate.model.devices.daq.daq_synthetic
module
navigate.model.devices.filter_wheel
module
navigate.model.devices.filter_wheel.filter_wheel_asi
module
navigate.model.devices.filter_wheel.filter_wheel_base
module
navigate.model.devices.filter_wheel.filter_wheel_ludl
module
navigate.model.devices.filter_wheel.filter_wheel_sutter
module
navigate.model.devices.filter_wheel.filter_wheel_synthetic
module
navigate.model.devices.galvo
module
navigate.model.devices.galvo.galvo_base
module
navigate.model.devices.galvo.galvo_synthetic
module
navigate.model.devices.lasers
module
navigate.model.devices.lasers.laser_base
module
navigate.model.devices.lasers.laser_synthetic
module
navigate.model.devices.mirrors
module
navigate.model.devices.mirrors.mirror_base
module
navigate.model.devices.mirrors.mirror_imop
module
navigate.model.devices.mirrors.mirror_synthetic
module
navigate.model.devices.objectives
module
navigate.model.devices.remote_focus
module
navigate.model.devices.remote_focus.remote_focus_base
module
navigate.model.devices.remote_focus.remote_focus_synthetic
module
navigate.model.devices.shutter
module
navigate.model.devices.shutter.laser_shutter_base
module
navigate.model.devices.shutter.laser_shutter_synthetic
module
navigate.model.devices.stages
module
navigate.model.devices.stages.stage_asi
module
navigate.model.devices.stages.stage_asi_MFCTwoThousand
module
navigate.model.devices.stages.stage_asi_MSTwoThousand
module
navigate.model.devices.stages.stage_base
module
navigate.model.devices.stages.stage_mcl
module
navigate.model.devices.stages.stage_pi
module
navigate.model.devices.stages.stage_sutter
module
navigate.model.devices.stages.stage_synthetic
module
navigate.model.devices.stages.stage_tl_kcube_inertial
module
navigate.model.devices.stages.stage_tl_kcube_steppermotor
module
navigate.model.devices.zoom
module
navigate.model.devices.zoom.zoom_base
module
navigate.model.devices.zoom.zoom_dynamixel
module
navigate.model.devices.zoom.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.cva_conpro
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.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)
(navigate.model.devices.filter_wheel.filter_wheel_synthetic.SyntheticFilterWheel attribute)
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.camera_base.CameraBase property)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuBase property)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrca property)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaFire property)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaFusion property)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaLightning property)
(navigate.model.devices.camera.camera_synthetic.SyntheticCamera property)
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.laser_shutter_base.ShutterBase method)
(navigate.model.devices.shutter.laser_shutter_synthetic.SyntheticShutter method)
overlap (navigate.model.features.common_features.FindTissueSimple2D attribute)
(navigate.model.features.volume_search.VolumeSearch attribute)
OWNDATA (navigate.model.concurrency.concurrency_tools.SharedNDArray attribute)
P
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.stage_pi.PIStage attribute)
pi_device (navigate.model.devices.stages.stage_pi.PIStage attribute)
pi_tools (navigate.model.devices.stages.stage_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.stage_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)
plugin_devices (navigate.model.microscope.Microscope attribute)
plugins_path (navigate.model.plugins_model.PluginsModel 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.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.camera_synthetic.SyntheticCamera attribute)
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.cva_conpro.ConstantVelocityAcquisition 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.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.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.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.filter_wheel_sutter.SutterFilterWheel method)
(navigate.model.devices.filter_wheel.filter_wheel_synthetic.SyntheticFilterWheel method)
read_on_init (navigate.model.devices.filter_wheel.filter_wheel_sutter.SutterFilterWheel attribute)
read_position() (navigate.model.devices.zoom.zoom_base.ZoomBase method)
(navigate.model.devices.zoom.zoom_dynamixel.DynamixelZoom method)
(navigate.model.devices.zoom.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)
real (navigate.model.concurrency.concurrency_tools.SharedNDArray attribute)
refresh_display() (navigate.model.devices.APIs.sutter.MP285.MP285 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_dict (navigate.controller.configuration_controller.ConfigurationController property)
remote_focus_max_voltage (navigate.model.devices.remote_focus.remote_focus_base.RemoteFocusBase attribute)
(navigate.model.devices.remote_focus.remote_focus_synthetic.SyntheticRemoteFocus attribute)
remote_focus_min_voltage (navigate.model.devices.remote_focus.remote_focus_base.RemoteFocusBase attribute)
(navigate.model.devices.remote_focus.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.remote_focus_base)
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_position() (navigate.model.devices.stages.stage_asi.ASIStage method)
(navigate.model.devices.stages.stage_asi_MSTwoThousand.ASIStage method)
(navigate.model.devices.stages.stage_mcl.MCLStage method)
(navigate.model.devices.stages.stage_pi.PIStage method)
(navigate.model.devices.stages.stage_sutter.SutterStage method)
(navigate.model.devices.stages.stage_synthetic.SyntheticStage method)
(navigate.model.devices.stages.stage_tl_kcube_inertial.TLKIMStage method)
(navigate.model.devices.stages.stage_tl_kcube_steppermotor.TLKSTStage method)
report_settings() (navigate.model.devices.camera.camera_hamamatsu.HamamatsuBase method)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrca method)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaFire method)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaFusion method)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaLightning method)
(navigate.model.devices.camera.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.stages.stage_sutter.SutterStage attribute)
(navigate.model.features.restful_features.IlastikSegmentation attribute)
resolution_mode (navigate.model.features.common_features.ChangeResolution 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.daq_synthetic.SyntheticDAQ method)
(navigate.model.model.Model method)
run_command() (navigate.model.model.Model method)
run_data_process() (navigate.model.model.Model method)
run_homing() (navigate.model.devices.stages.stage_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)
sample_rate (navigate.model.devices.daq.daq_base.DAQBase attribute)
(navigate.model.devices.daq.daq_synthetic.SyntheticDAQ attribute)
(navigate.model.devices.galvo.galvo_base.GalvoBase attribute)
(navigate.model.devices.galvo.galvo_synthetic.SyntheticGalvo attribute)
(navigate.model.devices.remote_focus.remote_focus_base.RemoteFocusBase attribute)
(navigate.model.devices.remote_focus.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.mirror_imop.ImagineOpticsMirror method)
save_yaml_file() (in module navigate.tools.file_functions)
saving_flags (navigate.model.features.image_writer.ImageWriter attribute)
sawtooth() (in module navigate.model.waveforms)
scan_axis_triggered_move() (navigate.model.devices.stages.stage_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.stage_asi.ASIStage method)
(navigate.model.devices.stages.stage_asi_MSTwoThousand.ASIStage method)
(navigate.model.devices.stages.stage_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.stage_asi.ASIStage method)
(navigate.model.devices.stages.stage_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)
send_filter_wheel_command() (navigate.model.devices.APIs.asi.asi_MFC_controller.MFCTwoThousand method)
(navigate.model.devices.APIs.asi.asi_tiger_controller.TigerController method)
serial (navigate.model.devices.filter_wheel.filter_wheel_ludl.LUDLFilterWheel attribute)
(navigate.model.devices.filter_wheel.filter_wheel_sutter.SutterFilterWheel attribute)
serial_number (navigate.model.devices.camera.camera_hamamatsu.HamamatsuBase property)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrca property)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaFire property)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaFusion property)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaLightning property)
(navigate.model.devices.camera.camera_synthetic.SyntheticCamera attribute)
(navigate.model.devices.stages.stage_tl_kcube_inertial.TLKIMStage attribute)
(navigate.model.devices.stages.stage_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.camera_hamamatsu.HamamatsuBase method)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrca method)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaFire method)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaFusion method)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaLightning method)
(navigate.model.devices.camera.camera_synthetic.SyntheticCamera 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.camera_hamamatsu.HamamatsuBase method)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrca method)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaFire method)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaFusion method)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaLightning method)
(navigate.model.devices.camera.camera_synthetic.SyntheticCamera method)
set_external_trigger() (navigate.model.devices.daq.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.filter_wheel_asi.ASIFilterWheel method)
(navigate.model.devices.filter_wheel.filter_wheel_ludl.LUDLFilterWheel method)
(navigate.model.devices.filter_wheel.filter_wheel_sutter.SutterFilterWheel method)
(navigate.model.devices.filter_wheel.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.mirror_imop.ImagineOpticsMirror method)
set_laser_operating_mode() (navigate.model.devices.APIs.coherent.ObisLaser.ObisLaser method)
set_line_interval() (navigate.model.devices.camera.camera_hamamatsu.HamamatsuBase method)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrca method)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaFire method)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaFusion method)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaLightning method)
(navigate.model.devices.camera.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.mirror_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.laser_base.LaserBase method)
(navigate.model.devices.lasers.laser_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.camera_synthetic.SyntheticCameraController method)
set_readout_direction() (navigate.model.devices.camera.camera_base.CameraBase method)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuBase method)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrca method)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaFire method)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaFusion method)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaLightning method)
(navigate.model.devices.camera.camera_synthetic.SyntheticCamera method)
set_resolution_and_velocity() (navigate.model.devices.APIs.sutter.MP285.MP285 method)
set_ROI() (navigate.model.devices.camera.camera_hamamatsu.HamamatsuBase method)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrca method)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaFire method)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaFusion method)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaLightning method)
(navigate.model.devices.camera.camera_synthetic.SyntheticCamera method)
set_sensor_mode() (navigate.model.devices.camera.camera_hamamatsu.HamamatsuBase method)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrca method)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaFire method)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaFusion method)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaLightning method)
(navigate.model.devices.camera.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.stage_asi.ASIStage method)
(navigate.model.devices.stages.stage_asi_MSTwoThousand.ASIStage method)
(navigate.model.devices.stages.stage_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.zoom_base.ZoomBase method)
(navigate.model.devices.zoom.zoom_dynamixel.DynamixelZoom method)
(navigate.model.devices.zoom.zoom_synthetic.SyntheticZoom method)
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_state (navigate.model.devices.shutter.laser_shutter_base.ShutterBase attribute)
(navigate.model.devices.shutter.laser_shutter_synthetic.SyntheticShutter attribute)
ShutterBase (class in navigate.model.devices.shutter.laser_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.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.filter_wheel_ludl.LUDLFilterWheel attribute)
size (navigate.model.concurrency.concurrency_tools.SharedNDArray attribute)
sleeptime (navigate.model.devices.zoom.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.filter_wheel.filter_wheel_sutter.SutterFilterWheel attribute)
(navigate.model.devices.stages.stage_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.stage_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.stage_asi.ASIStage attribute)
(navigate.model.devices.stages.stage_asi_MSTwoThousand.ASIStage attribute)
(navigate.model.devices.stages.stage_base.StageBase attribute)
(navigate.model.devices.stages.stage_mcl.MCLStage attribute)
(navigate.model.devices.stages.stage_pi.PIStage attribute)
(navigate.model.devices.stages.stage_sutter.SutterStage attribute)
(navigate.model.devices.stages.stage_synthetic.SyntheticStage attribute)
(navigate.model.devices.stages.stage_tl_kcube_inertial.TLKIMStage attribute)
(navigate.model.devices.stages.stage_tl_kcube_steppermotor.TLKSTStage attribute)
stage_flip_flags (navigate.controller.configuration_controller.ConfigurationController property)
stage_limits (navigate.model.devices.stages.stage_asi.ASIStage attribute)
(navigate.model.devices.stages.stage_asi_MSTwoThousand.ASIStage attribute)
(navigate.model.devices.stages.stage_base.StageBase attribute)
(navigate.model.devices.stages.stage_mcl.MCLStage attribute)
(navigate.model.devices.stages.stage_pi.PIStage attribute)
(navigate.model.devices.stages.stage_sutter.SutterStage attribute)
(navigate.model.devices.stages.stage_synthetic.SyntheticStage attribute)
(navigate.model.devices.stages.stage_tl_kcube_inertial.TLKIMStage attribute)
(navigate.model.devices.stages.stage_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.stage_sutter.SutterStage attribute)
stage_y_pos (navigate.model.devices.stages.stage_sutter.SutterStage attribute)
stage_z_pos (navigate.model.devices.stages.stage_sutter.SutterStage attribute)
StageBase (class in navigate.model.devices.stages.stage_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.stage_asi.ASIStage method)
(navigate.model.devices.stages.stage_asi_MSTwoThousand.ASIStage method)
(navigate.model.devices.stages.stage_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.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.laser_shutter_base.ShutterBase property)
(navigate.model.devices.shutter.laser_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.camera_base.CameraBase attribute)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuBase attribute)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrca attribute)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaFire attribute)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaFusion attribute)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaLightning attribute)
(navigate.model.devices.camera.camera_synthetic.SyntheticCamera attribute)
step_image_width (navigate.model.devices.camera.camera_base.CameraBase attribute)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuBase attribute)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrca attribute)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaFire attribute)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaFusion attribute)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaLightning attribute)
(navigate.model.devices.camera.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.stage_asi.ASIStage method)
(navigate.model.devices.stages.stage_asi_MSTwoThousand.ASIStage method)
(navigate.model.devices.stages.stage_base.StageBase method)
(navigate.model.devices.stages.stage_mcl.MCLStage method)
(navigate.model.devices.stages.stage_pi.PIStage method)
(navigate.model.devices.stages.stage_sutter.SutterStage method)
(navigate.model.devices.stages.stage_synthetic.SyntheticStage method)
(navigate.model.devices.stages.stage_tl_kcube_inertial.TLKIMStage method)
(navigate.model.devices.stages.stage_tl_kcube_steppermotor.TLKSTStage method)
stop_acquisition (navigate.model.model.Model attribute)
stop_acquisition() (navigate.model.devices.daq.daq_synthetic.SyntheticDAQ method)
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.stage_asi.ASIStage method)
(navigate.model.devices.stages.stage_asi_MSTwoThousand.ASIStage method)
(navigate.model.devices.stages.stage_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.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.filter_wheel_sutter)
SutterStage (class in navigate.model.devices.stages.stage_sutter)
swapaxes() (navigate.model.concurrency.concurrency_tools.SharedNDArray method)
sweep_time (navigate.model.devices.galvo.galvo_base.GalvoBase attribute)
(navigate.model.devices.galvo.galvo_synthetic.SyntheticGalvo attribute)
(navigate.model.devices.remote_focus.remote_focus_base.RemoteFocusBase attribute)
(navigate.model.devices.remote_focus.remote_focus_synthetic.SyntheticRemoteFocus attribute)
sweep_times (navigate.model.devices.daq.daq_base.DAQBase attribute)
(navigate.model.devices.daq.daq_synthetic.SyntheticDAQ attribute)
SynchronizedThreadPool (class in navigate.controller.thread_pool)
SyntheticCamera (class in navigate.model.devices.camera.camera_synthetic)
SyntheticCameraController (class in navigate.model.devices.camera.camera_synthetic)
SyntheticDAQ (class in navigate.model.devices.daq.daq_synthetic)
SyntheticFilterWheel (class in navigate.model.devices.filter_wheel.filter_wheel_synthetic)
SyntheticGalvo (class in navigate.model.devices.galvo.galvo_synthetic)
SyntheticLaser (class in navigate.model.devices.lasers.laser_synthetic)
SyntheticMirror (class in navigate.model.devices.mirrors.mirror_synthetic)
SyntheticRemoteFocus (class in navigate.model.devices.remote_focus.remote_focus_synthetic)
SyntheticShutter (class in navigate.model.devices.shutter.laser_shutter_synthetic)
SyntheticStage (class in navigate.model.devices.stages.stage_synthetic)
SyntheticZoom (class in navigate.model.devices.zoom.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)
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.filter_wheel_ludl)
(in module navigate.model.devices.filter_wheel.filter_wheel_sutter)
(navigate.model.devices.zoom.zoom_dynamixel.DynamixelZoom attribute)
TLKIMStage (class in navigate.model.devices.stages.stage_tl_kcube_inertial)
TLKSTStage (class in navigate.model.devices.stages.stage_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)
torque_disable (navigate.model.devices.zoom.zoom_dynamixel.DynamixelZoom attribute)
torque_enable (navigate.model.devices.zoom.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.daq_synthetic.SyntheticDAQ attribute)
turn_off() (navigate.model.devices.APIs.coherent.ObisLaser.ObisLaser method)
(navigate.model.devices.APIs.omicron.LuxxLaser.LuxxLaser method)
(navigate.model.devices.galvo.galvo_base.GalvoBase method)
(navigate.model.devices.galvo.galvo_synthetic.SyntheticGalvo method)
(navigate.model.devices.lasers.laser_base.LaserBase method)
(navigate.model.devices.lasers.laser_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.laser_base.LaserBase method)
(navigate.model.devices.lasers.laser_synthetic.SyntheticLaser method)
turn_on_laser() (navigate.model.microscope.Microscope method)
U
unload_sample() (navigate.model.devices.stages.stage_synthetic.SyntheticStage method)
unlock() (navigate.controller.thread_pool.SelfLockThread method)
update_analog_task() (navigate.model.devices.daq.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.camera_base.CameraBase property)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuBase property)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrca property)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaFire property)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaFusion property)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaLightning property)
(navigate.model.devices.camera.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.stage_asi.ASIStage method)
(navigate.model.devices.stages.stage_asi_MSTwoThousand.ASIStage method)
(navigate.model.devices.stages.stage_base.StageBase method)
(navigate.model.devices.stages.stage_mcl.MCLStage method)
(navigate.model.devices.stages.stage_pi.PIStage method)
(navigate.model.devices.stages.stage_sutter.SutterStage method)
(navigate.model.devices.stages.stage_synthetic.SyntheticStage method)
(navigate.model.devices.stages.stage_tl_kcube_inertial.TLKIMStage method)
(navigate.model.devices.stages.stage_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.stage_asi.ASIStage method)
(navigate.model.devices.stages.stage_asi_MSTwoThousand.ASIStage method)
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.stage_pi.PIStage method)
wait_to_run_lock (navigate.model.devices.daq.daq_synthetic.SyntheticDAQ attribute)
wait_until_done (navigate.model.devices.filter_wheel.filter_wheel_sutter.SutterFilterWheel attribute)
wait_until_done_delay (navigate.model.devices.filter_wheel.filter_wheel_asi.ASIFilterWheel attribute)
(navigate.model.devices.filter_wheel.filter_wheel_ludl.LUDLFilterWheel attribute)
(navigate.model.devices.filter_wheel.filter_wheel_sutter.SutterFilterWheel attribute)
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.daq_base.DAQBase attribute)
(navigate.model.devices.daq.daq_synthetic.SyntheticDAQ attribute)
waveform_dict (navigate.model.devices.daq.daq_base.DAQBase attribute)
(navigate.model.devices.daq.daq_synthetic.SyntheticDAQ attribute)
(navigate.model.devices.galvo.galvo_base.GalvoBase attribute)
(navigate.model.devices.galvo.galvo_synthetic.SyntheticGalvo attribute)
(navigate.model.devices.remote_focus.remote_focus_base.RemoteFocusBase attribute)
(navigate.model.devices.remote_focus.remote_focus_synthetic.SyntheticRemoteFocus attribute)
waveform_expand_num (navigate.model.devices.daq.daq_base.DAQBase attribute)
(navigate.model.devices.daq.daq_synthetic.SyntheticDAQ attribute)
waveform_repeat_num (navigate.model.devices.daq.daq_base.DAQBase attribute)
(navigate.model.devices.daq.daq_synthetic.SyntheticDAQ attribute)
wheel_position (navigate.model.devices.filter_wheel.filter_wheel_asi.ASIFilterWheel attribute)
(navigate.model.devices.filter_wheel.filter_wheel_base.FilterWheelBase attribute)
(navigate.model.devices.filter_wheel.filter_wheel_ludl.LUDLFilterWheel attribute)
(navigate.model.devices.filter_wheel.filter_wheel_sutter.SutterFilterWheel attribute)
(navigate.model.devices.filter_wheel.filter_wheel_synthetic.SyntheticFilterWheel attribute)
,
[1]
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_waveforms_to_tasks() (navigate.model.devices.daq.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_pixels (navigate.model.devices.camera.camera_base.CameraBase attribute)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuBase attribute)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrca attribute)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaFire attribute)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaFusion attribute)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaLightning attribute)
(navigate.model.devices.camera.camera_synthetic.SyntheticCamera attribute)
XMLMetadata (class in navigate.model.metadata_sources.metadata)
Y
y_pixels (navigate.model.devices.camera.camera_base.CameraBase attribute)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuBase attribute)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrca attribute)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaFire attribute)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaFusion attribute)
(navigate.model.devices.camera.camera_hamamatsu.HamamatsuOrcaLightning attribute)
(navigate.model.devices.camera.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.mirror_imop.ImagineOpticsMirror method)
zoom (navigate.model.features.restful_features.IlastikSegmentation attribute)
zoom_value (navigate.model.features.common_features.ChangeResolution attribute)
ZoomBase (class in navigate.model.devices.zoom.zoom_base)
zoomdict (navigate.model.devices.zoom.zoom_base.ZoomBase attribute)
(navigate.model.devices.zoom.zoom_dynamixel.DynamixelZoom attribute)
(navigate.model.devices.zoom.zoom_synthetic.SyntheticZoom attribute)
zoomvalue (navigate.model.devices.zoom.zoom_base.ZoomBase attribute)
(navigate.model.devices.zoom.zoom_dynamixel.DynamixelZoom attribute)
(navigate.model.devices.zoom.zoom_synthetic.SyntheticZoom attribute)
ZStackAcquisition (class in navigate.model.features.common_features)