================ Popups And Tools ================ This page documents popup windows and utility dialogs used across **navigate**. .. _ui_file_save_dialog: File Saving Dialog (Misc. Notes Tab) ==================================== .. image:: ../../images/popup_save_dialog_misc_notes.png :align: center :alt: File Saving Dialog popup showing the Misc. Notes tab. This dialog appears when acquisition starts in a save-enabled mode (non-continuous) with :ref:`Save Data ` enabled. You can provide text in the :guilabel:`Misc. Notes` field to be saved alongside acquisition metadata. .. _ui_file_save_dialog_bdv: File Saving Dialog (BDV Settings Tab) ===================================== .. image:: ../../images/popup_save_dialog_bdv_settings.png :align: center :alt: File Saving Dialog popup showing the BDV Settings tab. Use this tab to configure BDV-related shear, rotation, and downsampling metadata. This information will be saved in the BDV XML file alongside acquired data when :ref:`Save Data ` is enabled, enabling the correct spatial interpretation of your data in BDV and compatible tools. More about BDV can be found on the ImageJ website: https://imagej.net/plugins/bdv/. .. _ui_autofocus: Autofocus Settings ================== .. image:: ../../images/popup_autofocus_settings.png :align: center :alt: Autofocus Settings popup. This popup configures autofocus behavior used by :ref:`features `. You can open it from :ref:`Quick Launch Buttons ` or from the :menuselection:`Autofocus` menu. By default, autofocus runs in two passes: one coarse and one fine. The coarse pass uses larger step sizes to locate the best focus region, and the fine pass searches locally around that coarse peak. If the peak lies outside the defined search range, the routine currently does not expand the range automatically. The routine can run on different focusing axes when compatible stage hardware is available. To run autofocus, press :guilabel:`Start Autofocus`. The focus metric is the Shannon entropy of the discrete cosine transform, which is used to find the region of highest contrast (best focus). Spline-fit and test-significance buttons are already present in preparation for additional intelligent autofocus functionality in future updates. .. _ui_waveform_parameters: Waveform Parameters =================== .. image:: ../../images/popup_waveform_parameters.png :align: center :alt: Waveform Parameter Settings popup. Use this popup to configure waveform amplitudes, offsets, timing, and smoothing used by :ref:`Waveform Settings `. Advanced Galvo Setting ====================== .. image:: ../../images/popup_advanced_waveform_channel_1.png :align: center :alt: Advanced Galvo Setting popup showing the Channel 1 tab. This advanced popup is opened from Waveform Parameters and provides channel-specific galvo amplitude and offset settings. When more than one channel is configured, each channel's settings are shown on a separate tab. .. _ui_configure_microscopes: Configure Microscopes ===================== .. image:: ../../images/popup_configure_microscopes.png :align: center :alt: Configure Microscopes popup. Open this popup from :menuselection:`Microscope Configuration --> Configure Microscope` in :ref:`ui_microscope_configuration`. This window selects the primary microscope and helps inspect multi-microscope hardware assignments. Advanced Stage Parameters ========================= .. image:: ../../images/popup_advanced_stage_parameters.png :align: center :alt: Advanced Stage Parameters popup. Open this popup from :menuselection:`Stage Control --> Advanced Stage Parameters`. It is useful for configuring stage limits, stage home/offset values, and axis flip flags used to align microscope coordinate behavior. For coordinate-system setup guidance, see :ref:`coordinate_system`. .. _ui_multiposition_tiling_wizard: Tiling Wizard ============= .. image:: ../../images/popup_tiling_wizard.png :align: center :alt: Multi-Position Tiling Wizard popup. The tiling wizard calculates tiled position grids from start/end coordinates, field-of-view size, and overlap. Open it from :ref:`ui_multiposition_buttons` in :ref:`ui_multiposition`. 1. Set axis start and end positions. 2. Confirm FOV distance and overlap. 3. Click :guilabel:`Populate Multi-Position Table`. Advanced Camera Settings ======================== .. image:: ../../images/popup_advanced_camera_settings.png :align: center :alt: Advanced Camera Settings popup. Use this popup for advanced camera control options, including microscope selection and image-direction settings. Camera Map Settings =================== .. image:: ../../images/popup_camera_map_settings.png :align: center :alt: Camera Map Settings popup. This popup supports loading dark-frame stacks and generating camera offset/variance maps. More information can be found in the :ref:`SNR Visualization Mode ` section of the developer deep dive. .. _ui_performance_diagnostics: Performance Diagnostics ======================= .. image:: ../../images/popup_performance_diagnostics.png :align: center :alt: Performance Diagnostics popup window. Open from :menuselection:`File --> Performance Diagnostics` to inspect acquisition, display, and histogram timing behavior. Adaptive Optics =============== .. image:: ../../images/popup_adaptive_optics_tony_wilson.png :align: center :alt: Adaptive Optics popup showing the Tony Wilson tab. This tab contains iterative optimization controls and mode selection for adaptive optics routines. Adaptive Optics (CNN-AO Tab) ============================ .. image:: ../../images/popup_adaptive_optics_cnn_ao.png :align: center :alt: Adaptive Optics popup showing the CNN-AO tab. The CNN-AO tab provides model-based adaptive optics controls within the same popup. Feature List Popup ================== .. image:: ../../images/popup_feature_list.png :align: center :alt: Feature List popup for creating or editing feature lists. Use this popup to create feature lists, preview graph layout, and edit serialized feature content. Feature Config Popup ==================== .. image:: ../../images/popup_feature_config.png :align: center :alt: Feature Configuration popup for editing feature node parameters. This popup configures the selected feature node and its arguments. Feature Advanced Settings Popup =============================== .. image:: ../../images/popup_feature_advanced_settings.png :align: center :alt: Feature Advanced Settings popup. Use this popup to define and save advanced parameter mappings for feature arguments. Ilastik Settings ================ .. image:: ../../images/popup_ilastik_settings.png :align: center :alt: Ilastik Settings popup. This popup configures ilastik project integration, target labels, and segmentation usage options. Plugins Popup ============= .. image:: ../../images/popup_plugins.png :align: center :alt: Plugins popup used for plugin uninstall management. This popup lists installed plugins and supports uninstall operations.