├── .github ├── ISSUE_TEMPLATE │ ├── feature_request.md │ └── issue-report.md └── workflows │ ├── black.yml │ ├── build_docs.yaml │ ├── deploy.yml │ └── push_checks.yaml ├── .gitignore ├── .pre-commit-config.yaml ├── LICENSE.md ├── MANIFEST.in ├── README.md ├── codecov.yml ├── docs ├── Makefile ├── capture_gui.py ├── make.bat ├── source │ ├── 01_getting_started │ │ ├── 01_quick_start │ │ │ ├── 01_quick_start.rst │ │ │ └── images │ │ │ │ └── save_dialog.png │ │ ├── 02_software_installation │ │ │ └── 02_software_installation.rst │ │ └── 03_i_want_to │ │ │ ├── 03_i_want_to.rst │ │ │ ├── add_new_device.rst │ │ │ ├── advanced.rst │ │ │ ├── beginner.rst │ │ │ ├── images │ │ │ ├── beginner │ │ │ │ ├── ROI-definition.png │ │ │ │ ├── channel-selector-filter.png │ │ │ │ ├── channel-selector.png │ │ │ │ ├── continuous-scan-acquire.png │ │ │ │ ├── continuous-scan-dropdown.png │ │ │ │ ├── continuous-scan-sample.png │ │ │ │ ├── define-step-size.png │ │ │ │ ├── laser-cycling-settings.png │ │ │ │ ├── open-navigate.png │ │ │ │ ├── press-end-pos.png │ │ │ │ ├── press-start-pos.png │ │ │ │ ├── save-data.png │ │ │ │ ├── save-dialog-box-acquire.png │ │ │ │ ├── save-dialog-box.png │ │ │ │ ├── sensor-mode.png │ │ │ │ ├── single-acquisition-acquire.png │ │ │ │ ├── single-acquisition-dropdown.png │ │ │ │ ├── single-acquisition.png │ │ │ │ ├── stage-control-end-pos-zstack.png │ │ │ │ ├── stage-control-start-pos-zstack.png │ │ │ │ ├── stage-movement-panel.png │ │ │ │ ├── stop-acquisition.png │ │ │ │ └── z-stack-acquisition.png │ │ │ ├── feature_gui_1.png │ │ │ ├── feature_gui_10.png │ │ │ ├── feature_gui_2.png │ │ │ ├── feature_gui_3.png │ │ │ ├── feature_gui_4.png │ │ │ ├── feature_gui_5.png │ │ │ ├── feature_gui_6.png │ │ │ ├── feature_gui_7.png │ │ │ ├── feature_gui_8.png │ │ │ ├── feature_gui_9.png │ │ │ └── intermediate │ │ │ │ ├── multiposition_empty.png │ │ │ │ └── multiposition_tissue.png │ │ │ └── intermediate.rst │ ├── 02_user_guide │ │ ├── 01_supported_hardware │ │ │ ├── camera.rst │ │ │ ├── daq.rst │ │ │ ├── dcam_api.rst │ │ │ ├── deformable_mirror.rst │ │ │ ├── dichroic.rst │ │ │ ├── filter_wheel.rst │ │ │ ├── galvo.rst │ │ │ ├── hardware_home.rst │ │ │ ├── images │ │ │ │ ├── 6259_pinout.png │ │ │ │ ├── 6723_pinout.png │ │ │ │ └── 6738_pinout.png │ │ │ ├── laser.rst │ │ │ ├── pvcam.rst │ │ │ ├── remote_focus.rst │ │ │ ├── shutter.rst │ │ │ ├── stage.rst │ │ │ └── zoom.rst │ │ ├── 02_file_formats │ │ │ └── file_formats.rst │ │ ├── 03_user_interface_walkthrough │ │ │ ├── images │ │ │ │ ├── autofocus_settings.png │ │ │ │ ├── configure_microscopes.png │ │ │ │ ├── display_camera.png │ │ │ │ ├── display_waveform.png │ │ │ │ ├── home_screen.png │ │ │ │ ├── menu_autofocus.png │ │ │ │ ├── menu_features.png │ │ │ │ ├── menu_file.png │ │ │ │ ├── menu_microscope_configuration.png │ │ │ │ ├── menu_plugins.png │ │ │ │ ├── menu_stage_control.png │ │ │ │ ├── menu_window.png │ │ │ │ ├── multiposition_right_click.png │ │ │ │ ├── popout_right_click.png │ │ │ │ ├── popout_stage.png │ │ │ │ ├── save_dialog.png │ │ │ │ ├── settings_camera.png │ │ │ │ ├── settings_channels.png │ │ │ │ ├── settings_multiposition.png │ │ │ │ ├── settings_stage.png │ │ │ │ ├── tiling_wizard.png │ │ │ │ └── waveform_parameters.png │ │ │ └── user_interface_walkthrough.rst │ │ ├── 04_microscope_setup │ │ │ ├── 01_software_configuration │ │ │ │ ├── images │ │ │ │ │ └── configurator.PNG │ │ │ │ └── software_configuration.rst │ │ │ ├── 02_multiple_cameras │ │ │ │ ├── images │ │ │ │ │ ├── multi_cams_1.png │ │ │ │ │ ├── multi_cams_2.png │ │ │ │ │ ├── multi_cams_3.png │ │ │ │ │ ├── multi_cams_4.png │ │ │ │ │ ├── multi_cams_5.png │ │ │ │ │ ├── multi_cams_6.png │ │ │ │ │ ├── multi_cams_7.png │ │ │ │ │ ├── multi_cams_8.png │ │ │ │ │ └── multi_cams_9.png │ │ │ │ └── multiple_cameras.rst │ │ │ ├── 03_snr │ │ │ │ └── snr.rst │ │ │ └── setup_microscope.rst │ │ ├── 05_acquiring_data │ │ │ ├── 01_acquiring_guide │ │ │ │ └── 01_acquiring_guide.rst │ │ │ ├── 02_feature_container │ │ │ │ ├── features.rst │ │ │ │ └── images │ │ │ │ │ ├── step_10.png │ │ │ │ │ ├── step_11.png │ │ │ │ │ ├── step_12.png │ │ │ │ │ ├── step_13.png │ │ │ │ │ ├── step_14.png │ │ │ │ │ ├── step_15.png │ │ │ │ │ ├── step_16.png │ │ │ │ │ ├── step_17.png │ │ │ │ │ ├── step_18.png │ │ │ │ │ ├── step_19.png │ │ │ │ │ ├── step_20.png │ │ │ │ │ ├── step_3.png │ │ │ │ │ ├── step_4.png │ │ │ │ │ ├── step_5.png │ │ │ │ │ ├── step_6.png │ │ │ │ │ ├── step_7.png │ │ │ │ │ ├── step_8.png │ │ │ │ │ └── step_9.png │ │ │ ├── 03_example_features │ │ │ │ └── example_feature_lists.rst │ │ │ ├── 04_current_features │ │ │ │ └── current_features.rst │ │ │ └── acquiring_home.rst │ │ └── 06_case_studies │ │ │ ├── 06_human_in_the_loop │ │ │ ├── human_in_the_loop.rst │ │ │ └── images │ │ │ │ ├── Picture1.png │ │ │ │ ├── Picture2.png │ │ │ │ ├── Picture3.png │ │ │ │ ├── Picture4.png │ │ │ │ └── Picture5.png │ │ │ ├── 07_smart_tiling │ │ │ ├── images │ │ │ │ ├── Picture1.png │ │ │ │ └── Picture2.png │ │ │ └── smart_tiling.rst │ │ │ ├── 08_smart_object_detection │ │ │ ├── images │ │ │ │ ├── Picture1.png │ │ │ │ ├── Picture2.png │ │ │ │ ├── Picture3.png │ │ │ │ ├── Picture4.png │ │ │ │ ├── Picture6.png │ │ │ │ ├── Picture7.png │ │ │ │ ├── Picture8.png │ │ │ │ └── Screenshot 2025-04-16 at 7.59.52 AM.png │ │ │ └── smart_object_detection.rst │ │ │ ├── acquire_CT-ASLM-V1_and_CT-ASLM-V2.rst │ │ │ ├── acquire_exASLM.rst │ │ │ ├── acquire_mesospimbt.rst │ │ │ ├── case_studies_home.rst │ │ │ ├── ilastik_segmentation.rst │ │ │ ├── images │ │ │ ├── autofocus_image.png │ │ │ ├── autofocus_settings.png │ │ │ ├── autofocus_settings_partial.png │ │ │ ├── find_sample.png │ │ │ ├── ilastik_1.png │ │ │ ├── ilastik_10.png │ │ │ ├── ilastik_11.png │ │ │ ├── ilastik_12.png │ │ │ ├── ilastik_13.png │ │ │ ├── ilastik_2.png │ │ │ ├── ilastik_3.png │ │ │ ├── ilastik_4.png │ │ │ ├── ilastik_5.png │ │ │ ├── ilastik_6.png │ │ │ ├── ilastik_7.png │ │ │ ├── ilastik_8.png │ │ │ ├── ilastik_9.png │ │ │ ├── meso_beam_1.png │ │ │ ├── meso_beam_10.png │ │ │ ├── meso_beam_11.png │ │ │ ├── meso_beam_12.png │ │ │ ├── meso_beam_13.png │ │ │ ├── meso_beam_14.png │ │ │ ├── meso_beam_15.png │ │ │ ├── meso_beam_2.png │ │ │ ├── meso_beam_3.png │ │ │ ├── meso_beam_4.png │ │ │ ├── meso_beam_5.png │ │ │ ├── meso_beam_6.png │ │ │ ├── meso_beam_7.png │ │ │ ├── meso_beam_8.png │ │ │ ├── meso_beam_9.png │ │ │ ├── multiposition_table.png │ │ │ ├── save_dialog.png │ │ │ ├── set_end_pos.png │ │ │ ├── set_start_pos.png │ │ │ └── tiling_wizard.png │ │ │ └── setup_voodoo.rst │ ├── 03_contributing │ │ ├── 01_contributing_guidelines │ │ │ └── 01_contributing_guidelines.rst │ │ ├── 02_developer_install │ │ │ └── 02_developer_install.rst │ │ ├── 03_software_architecture │ │ │ ├── images │ │ │ │ └── architecture.png │ │ │ └── software_architecture.rst │ │ ├── 04_feature_container │ │ │ ├── feature_container.rst │ │ │ └── images │ │ │ │ ├── step_1.png │ │ │ │ └── step_2.png │ │ ├── 05_restapi │ │ │ └── restapi.rst │ │ └── 06_plugin │ │ │ ├── images │ │ │ ├── plugin_1.png │ │ │ ├── plugin_2.png │ │ │ ├── plugin_3.png │ │ │ ├── plugin_4.png │ │ │ ├── plugin_5.png │ │ │ └── plugin_6.png │ │ │ └── plugin_home.rst │ ├── 04_faq │ │ ├── issues │ │ │ ├── 01_channel_switching.rst │ │ │ ├── 02_histogram.rst │ │ │ └── issues_home.rst │ │ └── troubleshooting │ │ │ ├── 01_proxy.rst │ │ │ ├── 02_usb_connectivity.rst │ │ │ └── troubleshooting_home.rst │ ├── 05_reference │ │ ├── api.rst │ │ └── implementations │ │ │ ├── configurations │ │ │ ├── configuration_OPMv2.yaml │ │ │ ├── configuration_OPMv3.yaml │ │ │ ├── configuration_biofrontiers.yaml │ │ │ ├── configuration_ctaslmv1.yaml │ │ │ ├── configuration_ctaslmv2.yaml │ │ │ ├── configuration_mesospimbt.yaml │ │ │ ├── configuration_multiscale.yaml │ │ │ ├── configuration_spectral_tirf.yaml │ │ │ ├── configuration_upright.yaml │ │ │ └── configuration_voodoo.yaml │ │ │ ├── images │ │ │ ├── ASLM.png │ │ │ ├── ao_opm.png │ │ │ ├── ctaslmv1.png │ │ │ ├── ctaslmv2.png │ │ │ ├── expansion_aslm.png │ │ │ ├── mct_aslm.png │ │ │ ├── robot.png │ │ │ ├── spectral_tirf.png │ │ │ └── tiling_opm.png │ │ │ └── implementations.rst │ ├── _templates │ │ ├── custom_class.rst │ │ └── custom_module.rst │ ├── conf.py │ └── index.rst └── test_docs.py ├── pyproject.toml ├── pytest.ini ├── src ├── __init__.py └── navigate │ ├── VERSION │ ├── __init__.py │ ├── _commit.py │ ├── config │ ├── __init__.py │ ├── config.py │ ├── configuration.yaml │ ├── configuration_database.py │ ├── experiment.yml │ ├── gui_configuration.yml │ ├── multi_positions.yml │ ├── rest_api_config.yml │ ├── synthetic_configuration.yaml │ ├── waveform_constants.yml │ └── waveform_templates.yml │ ├── controller │ ├── __init__.py │ ├── configuration_controller.py │ ├── configurator.py │ ├── controller.py │ ├── sub_controllers │ │ ├── __init__.py │ │ ├── acquire_bar.py │ │ ├── adaptive_optics.py │ │ ├── autofocus.py │ │ ├── camera_map.py │ │ ├── camera_settings.py │ │ ├── camera_view.py │ │ ├── channels_settings.py │ │ ├── channels_tab.py │ │ ├── diagnostics_popup.py │ │ ├── feature_advanced_setting.py │ │ ├── features_popup.py │ │ ├── gui.py │ │ ├── histogram.py │ │ ├── ilastik.py │ │ ├── keystrokes.py │ │ ├── menus.py │ │ ├── microscope_popup.py │ │ ├── multiposition.py │ │ ├── plugins.py │ │ ├── stages.py │ │ ├── stages_advanced.py │ │ ├── tiling.py │ │ ├── waveform_popup.py │ │ └── waveform_tab.py │ └── thread_pool.py │ ├── log_files │ ├── __init__.py │ ├── filters.py │ ├── log_functions.py │ └── logging.yml │ ├── main.py │ ├── model │ ├── __init__.py │ ├── analysis │ │ ├── __init__.py │ │ ├── boundary_detect.py │ │ ├── camera.py │ │ └── image_contrast.py │ ├── concurrency │ │ ├── __init__.py │ │ └── concurrency_tools.py │ ├── data_sources │ │ ├── __init__.py │ │ ├── bdv_data_source.py │ │ ├── data_source.py │ │ ├── pyramidal_data_source.py │ │ ├── tiff_data_source.py │ │ └── zarr_data_source.py │ ├── device_startup_functions.py │ ├── devices │ │ ├── APIs │ │ │ ├── __init__.py │ │ │ ├── asi │ │ │ │ ├── __init__.py │ │ │ │ ├── asi_MFC_controller.py │ │ │ │ ├── asi_MS2000_controller.py │ │ │ │ └── asi_tiger_controller.py │ │ │ ├── coherent │ │ │ │ ├── ObisLaser.py │ │ │ │ └── __init__.py │ │ │ ├── dynamixel │ │ │ │ ├── __init__.py │ │ │ │ ├── dxl_x64_c.dll │ │ │ │ ├── dxl_x64_c.lib │ │ │ │ └── dynamixel_functions.py │ │ │ ├── hamamatsu │ │ │ │ ├── HamamatsuAPI.py │ │ │ │ └── __init__.py │ │ │ ├── imagineoptics │ │ │ │ ├── __init__.py │ │ │ │ ├── c_interface_vc100_x64.dll │ │ │ │ ├── enums.py │ │ │ │ ├── imop.py │ │ │ │ └── mirao52e.dll │ │ │ ├── mcl │ │ │ │ ├── __init__.py │ │ │ │ └── madlib.py │ │ │ ├── omicron │ │ │ │ ├── LuxxLaser.py │ │ │ │ └── __init__.py │ │ │ ├── photometrics │ │ │ │ ├── PyVCAM-master │ │ │ │ │ ├── .gitignore │ │ │ │ │ ├── LICENSE │ │ │ │ │ ├── README.md │ │ │ │ │ ├── docs │ │ │ │ │ │ ├── CheetSheet.txt │ │ │ │ │ │ └── PyVCAM Wrapper.md │ │ │ │ │ ├── setup.py │ │ │ │ │ ├── src │ │ │ │ │ │ ├── constants_generator.py │ │ │ │ │ │ └── pyvcam │ │ │ │ │ │ │ ├── __init__.py │ │ │ │ │ │ │ ├── camera.py │ │ │ │ │ │ │ ├── constants.py │ │ │ │ │ │ │ ├── pvcmodule.cpp │ │ │ │ │ │ │ └── pvcmodule.h │ │ │ │ │ └── tests │ │ │ │ │ │ ├── camera_settings.py │ │ │ │ │ │ ├── change_settings_test.py │ │ │ │ │ │ ├── check_frame_status.py │ │ │ │ │ │ ├── live_mode.py │ │ │ │ │ │ ├── meta_data.py │ │ │ │ │ │ ├── multi_camera.py │ │ │ │ │ │ ├── multi_rois.py │ │ │ │ │ │ ├── newest_frame.py │ │ │ │ │ │ ├── seq_mode.py │ │ │ │ │ │ ├── single_image_polling.py │ │ │ │ │ │ ├── single_image_polling_show.py │ │ │ │ │ │ ├── stream_to_disk.py │ │ │ │ │ │ ├── sw_trigger.py │ │ │ │ │ │ └── test_camera.py │ │ │ │ ├── __init__.py │ │ │ │ └── use_photometrics_api.txt │ │ │ ├── pi │ │ │ │ ├── license.md │ │ │ │ └── readme.md │ │ │ ├── sutter │ │ │ │ ├── MP285.py │ │ │ │ └── __init__.py │ │ │ └── thorlabs │ │ │ │ ├── __init__.py │ │ │ │ ├── documentation │ │ │ │ ├── Thorlabs.MotionControl.KCube.InertialMotor.h │ │ │ │ └── Thorlabs.MotionControl.KCube.StepperMotor.h │ │ │ │ ├── kcube_inertial.py │ │ │ │ └── kcube_steppermotor.py │ │ ├── __init__.py │ │ ├── camera │ │ │ ├── __init__.py │ │ │ ├── base.py │ │ │ ├── daheng.py │ │ │ ├── hamamatsu.py │ │ │ ├── photometrics.py │ │ │ ├── synthetic.py │ │ │ └── ximea.py │ │ ├── daq │ │ │ ├── __init__.py │ │ │ ├── asi.py │ │ │ ├── base.py │ │ │ ├── ni.py │ │ │ └── synthetic.py │ │ ├── device_types.py │ │ ├── filter_wheel │ │ │ ├── __init__.py │ │ │ ├── asi.py │ │ │ ├── base.py │ │ │ ├── ludl.py │ │ │ ├── ni.py │ │ │ ├── sutter.py │ │ │ └── synthetic.py │ │ ├── galvo │ │ │ ├── __init__.py │ │ │ ├── asi.py │ │ │ ├── base.py │ │ │ ├── ni.py │ │ │ └── synthetic.py │ │ ├── laser │ │ │ ├── __init__.py │ │ │ ├── asi.py │ │ │ ├── base.py │ │ │ ├── ni.py │ │ │ └── synthetic.py │ │ ├── mirror │ │ │ ├── __init__.py │ │ │ ├── base.py │ │ │ ├── imop.py │ │ │ └── synthetic.py │ │ ├── objectives.py │ │ ├── pump │ │ │ ├── __init__.py │ │ │ └── tecan.py │ │ ├── remote_focus │ │ │ ├── __init__.py │ │ │ ├── asi.py │ │ │ ├── base.py │ │ │ ├── equipment_solutions.py │ │ │ ├── ni.py │ │ │ └── synthetic.py │ │ ├── shutter │ │ │ ├── __init__.py │ │ │ ├── asi.py │ │ │ ├── base.py │ │ │ ├── ni.py │ │ │ └── synthetic.py │ │ ├── stage │ │ │ ├── __init__.py │ │ │ ├── asi.py │ │ │ ├── base.py │ │ │ ├── conex.py │ │ │ ├── mcl.py │ │ │ ├── newport.py │ │ │ ├── ni.py │ │ │ ├── pi.py │ │ │ ├── sutter.py │ │ │ ├── synthetic.py │ │ │ └── thorlabs.py │ │ └── zoom │ │ │ ├── __init__.py │ │ │ ├── base.py │ │ │ ├── dynamixel.py │ │ │ └── synthetic.py │ ├── features │ │ ├── __init__.py │ │ ├── adaptive_optics.py │ │ ├── auto_tile_scan.py │ │ ├── autofocus.py │ │ ├── common_features.py │ │ ├── feature_container.py │ │ ├── feature_related_functions.py │ │ ├── image_writer.py │ │ ├── remove_empty_tiles.py │ │ ├── restful_features.py │ │ ├── update_setting.py │ │ └── volume_search.py │ ├── metadata_sources │ │ ├── __init__.py │ │ ├── bdv_metadata.py │ │ ├── metadata.py │ │ ├── ome_tiff_metadata.py │ │ └── zarr_metadata.py │ ├── microscope.py │ ├── model.py │ ├── plugins_model.py │ ├── utils │ │ ├── exceptions.py │ │ └── threads.py │ └── waveforms.py │ ├── plugins │ ├── __init__.py │ └── plugin_manager.py │ ├── tools │ ├── __init__.py │ ├── common_dict_tools.py │ ├── common_functions.py │ ├── decorators.py │ ├── file_functions.py │ ├── gui.py │ ├── image.py │ ├── linear_algebra.py │ ├── main_functions.py │ ├── multipos_table_tools.py │ ├── sdf.py │ ├── slicing.py │ ├── waveform_template_funcs.py │ └── xml_tools.py │ └── view │ ├── __init__.py │ ├── configurator_application_window.py │ ├── custom_widgets │ ├── ArrowLabel.py │ ├── CollapsibleFrame.py │ ├── DockableNotebook.py │ ├── LabelInputWidgetFactory.py │ ├── __init__.py │ ├── common.py │ ├── hover.py │ ├── popup.py │ ├── scrollbars.py │ └── validation.py │ ├── icon │ ├── mic.ico │ ├── mic.png │ ├── mic_orig.png │ └── splash_screen_image.png │ ├── main_application_window.py │ ├── main_window_content │ ├── __init__.py │ ├── acquire_notebook.py │ ├── camera_tab.py │ ├── channels_tab.py │ ├── display_notebook.py │ ├── images │ │ ├── cubic_bottom_to_top.png │ │ ├── cubic_top_to_bottom.png │ │ ├── d_down_1x_image.png │ │ ├── d_down_5x_image.png │ │ ├── d_down_5x_imageai.png │ │ ├── d_left_1x_image.png │ │ ├── d_left_5x_image.png │ │ ├── d_right_1x_image.png │ │ ├── d_right_5x_image.png │ │ ├── d_up_1x_image.png │ │ ├── d_up_5x_image.png │ │ ├── down_1x_image.png │ │ ├── down_5x_image.png │ │ ├── left_1x_image.png │ │ ├── left_5x_image.png │ │ ├── right_1x_image.png │ │ ├── right_5x_image.png │ │ ├── up_1x_image.png │ │ └── up_5x_image.png │ ├── menus.py │ ├── multiposition_tab.py │ ├── settings_notebook.py │ └── stage_tab.py │ ├── popups │ ├── __init__.py │ ├── acquire_popup.py │ ├── adaptiveoptics_popup.py │ ├── autofocus_setting_popup.py │ ├── camera_map_setting_popup.py │ ├── camera_setting_popup.py │ ├── camera_view_popup_window.py │ ├── diagnostics_popup.py │ ├── feature_list_popup.py │ ├── ilastik_setting_popup.py │ ├── microscope_setting_popup_window.py │ ├── plugins_popup.py │ ├── stages_advanced_popup.py │ ├── tiling_wizard_popup.py │ ├── tiling_wizard_popup2.py │ └── waveform_parameter_popup_window.py │ └── splash_screen.py └── test ├── __init__.py ├── config ├── test_config.py ├── test_configuration.py ├── test_experiment.py ├── test_rest_api_config.py ├── test_waveform_constants.py └── test_waveform_templates.py ├── conftest.py ├── controller ├── __init__.py ├── sub_controllers │ ├── __init__.py │ ├── test_acquire_bar.py │ ├── test_autofocus.py │ ├── test_camera_settings.py │ ├── test_camera_view.py │ ├── test_channels_settings.py │ ├── test_channels_tab.py │ ├── test_menus.py │ ├── test_multiposition.py │ ├── test_stages.py │ ├── test_tiling.py │ └── test_waveform_popup.py └── test_controller.py ├── log_files └── test_log_functions.py ├── model ├── __init__.py ├── analysis │ ├── __init__.py │ ├── test_boundary_detect.py │ └── test_camera.py ├── concurrency │ ├── __init__.py │ └── test_concurrency_tools.py ├── data_sources │ ├── test_bdv_data_source.py │ ├── test_data_source.py │ ├── test_tiff_data_source.py │ └── test_zarr_data_source.py ├── devices │ ├── APIs │ │ ├── __init__.py │ │ ├── coherent │ │ │ └── __init__.py │ │ ├── dynamixel │ │ │ └── __init__.py │ │ ├── hamamatsu │ │ │ ├── __init__.py │ │ │ └── test_hamamatsu_api.py │ │ ├── logitech │ │ │ └── __init__.py │ │ ├── omicron │ │ │ └── __init__.py │ │ ├── optotune │ │ │ └── __init__.py │ │ ├── pi │ │ │ └── __init__.py │ │ ├── sutter │ │ │ └── __init__.py │ │ └── thorlabs │ │ │ └── __init__.py │ ├── __init__.py │ ├── camera │ │ ├── __init__.py │ │ ├── test_camera_base.py │ │ ├── test_camera_synthetic.py │ │ ├── test_daheng.py │ │ └── test_hamamatsu.py │ ├── daq │ │ ├── test_daq_base.py │ │ ├── test_daq_ni.py │ │ └── test_daq_synthetic.py │ ├── filter_wheel │ │ ├── test_asi.py │ │ ├── test_fw_base.py │ │ ├── test_fw_synthetic.py │ │ └── test_sutter.py │ ├── galvo │ │ ├── test_galvo_base.py │ │ ├── test_galvo_ni.py │ │ └── test_galvo_synthetic.py │ ├── lasers │ │ ├── test_laser_base.py │ │ └── test_laser_ni.py │ ├── pump │ │ └── test_tecan.py │ ├── remote_focus │ │ ├── test_rf_base.py │ │ ├── test_rf_ni.py │ │ └── test_rf_synthetic.py │ ├── shutter │ │ ├── test_shutter_base.py │ │ ├── test_shutter_ni.py │ │ └── test_shutter_synthetic.py │ ├── stages │ │ ├── __init__.py │ │ ├── conftest.py │ │ ├── test_asi.py │ │ ├── test_mcl.py │ │ ├── test_pi.py │ │ ├── test_stage_base.py │ │ ├── test_stage_ni.py │ │ ├── test_sutter.py │ │ ├── test_tl_kcube_inertial.py │ │ └── test_tl_kcube_steppermotor.py │ ├── test_synthetic_hardware.py │ └── zoom │ │ ├── test_base.py │ │ ├── test_dynamixel.py │ │ └── test_synthetic.py ├── dummy.py ├── features │ ├── conftest.py │ ├── test_aslm_feature_container.py │ ├── test_autofocus.py │ ├── test_common_features.py │ ├── test_feature_related_functions.py │ ├── test_image_writer.py │ ├── test_restful_features.py │ └── test_volume_search.py ├── metadata_sources │ ├── test_bdv_metadata.py │ ├── test_metadata.py │ ├── test_ome_tiff_metadata.py │ └── test_zarr_metadata.py ├── test_aslm_analysis.py ├── test_device_startup_functions.py ├── test_microscope.py ├── test_model.py ├── test_plugins_model.py └── test_waveforms.py ├── plugins ├── __init__.py └── test_plugin_manager.py ├── test_commit.py ├── test_main.py ├── tools ├── __init__.py ├── test_common_dict_tools.py ├── test_common_functions.py ├── test_decorators.py ├── test_file_functions.py ├── test_image.py ├── test_linear_algebra.py ├── test_main_functions.py ├── test_multipos_table_tools.py ├── test_sdf.py ├── test_slicing.py ├── test_waveform_template_functs.py ├── test_xml_tools.py └── xml_examples │ ├── drosophila.xml │ └── samples-SP2.ome.xml └── view ├── __init__.py ├── custom_widgets ├── test_LabelInputWidgetFactory.py ├── test_hover.py └── test_validation.py ├── main_window_content ├── __init__.py ├── acquire_bar_frame │ ├── __init__.py │ └── test_acquirepopup.py ├── camera_display │ ├── __init__.py │ ├── camera_settings │ │ ├── __init__.py │ │ └── tabs │ │ │ └── __init__.py │ └── camera_view │ │ ├── __init__.py │ │ └── tabs │ │ └── __init__.py ├── stage_control │ ├── __init__.py │ └── tabs │ │ └── __init__.py └── tabs │ ├── __init__.py │ ├── advanced_settings │ └── __init__.py │ ├── channels │ └── __init__.py │ └── stage_control │ └── __init__.py ├── popups ├── __init__.py ├── test_autofocuspopup.py ├── test_feature_list_popup.py └── test_remotefocuspopup.py ├── test_main_application_window.py └── test_splash_screen.py /.github/ISSUE_TEMPLATE/feature_request.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheDeanLab/navigate/HEAD/.github/ISSUE_TEMPLATE/feature_request.md -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/issue-report.md: 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