.gitignore
AGENTS.md
CHANGES.md
CLAUDE.md
CONTRIBUTING.md
GETTING_STARTED.md
INSTALLATION.md
LICENSE
MANIFEST.in
README.md
RELEASE.md
SCRIPTING.md
mkdocs.yml
pyproject.toml
.claude/skills/linear/SKILL.md
.claude/skills/new-widget/SKILL.md
.claude/skills/review-changes/SKILL.md
.claude/skills/review-widget/SKILL.md
.github/workflows/publish.yml
.github/workflows/python-package.yml
docs/design/autofocus.md
docs/design/correlation-fm-surface-pre-correction.md
docs/design/odemis-fm-driver.md
docs/design/task-scheduling.md
example/autolamella.py
example/example.ipynb
example/example.py
example/example_imaging.py
example/example_milling.py
example/example_movement.py
example/example_notebook.ipynb
example/lithography.py
example/profile.npy
example/protocol_autolamella.yaml
example/protocol_lithography.yaml
example/protocol_slice_and_view.yaml
example/slice_and_view.py
examples/vertical_tab_widget_demo.py
examples/scripts/describe_lamellae.py
examples/scripts/export_summary.py
examples/scripts/survey_positions.py
external/application_files/autolamella.xml
external/application_files/cryo_Pt_dep.xml
fibsem/__init__.py
fibsem/_timing.py
fibsem/acquire.py
fibsem/calibration.py
fibsem/cancellation.py
fibsem/cli.py
fibsem/config.py
fibsem/configuration.py
fibsem/constants.py
fibsem/conversions.py
fibsem/gis.py
fibsem/guided_setup.py
fibsem/hooks.py
fibsem/logo.py
fibsem/manufacturers.py
fibsem/microscope.py
fibsem/movement.py
fibsem/projection.py
fibsem/scripting.py
fibsem/structures.py
fibsem/timing.py
fibsem/transformations.py
fibsem/update_check.py
fibsem/utils.py
fibsem/validation.py
fibsem/versioning.py
fibsem.egg-info/PKG-INFO
fibsem.egg-info/SOURCES.txt
fibsem.egg-info/dependency_links.txt
fibsem.egg-info/entry_points.txt
fibsem.egg-info/requires.txt
fibsem.egg-info/top_level.txt
fibsem/alignment/__init__.py
fibsem/alignment/methods.py
fibsem/alignment/plotting.py
fibsem/applications/__init__.py
fibsem/applications/autolamella/__init__.py
fibsem/applications/autolamella/config.py
fibsem/applications/autolamella/hook_defaults.py
fibsem/applications/autolamella/poses.py
fibsem/applications/autolamella/scripting.py
fibsem/applications/autolamella/structures.py
fibsem/applications/autolamella/task_outputs.py
fibsem/applications/autolamella/compat/notebook.ipynb
fibsem/applications/autolamella/compat/odemis.py
fibsem/applications/autolamella/protocol/.gitkeep
fibsem/applications/autolamella/protocol/__init__.py
fibsem/applications/autolamella/protocol/constants.py
fibsem/applications/autolamella/protocol/legacy.py
fibsem/applications/autolamella/protocol/task-protocol-waffle.yaml
fibsem/applications/autolamella/protocol/task-protocol.yaml
fibsem/applications/autolamella/protocol/validation.py
fibsem/applications/autolamella/protocol/development/task-protocol-coincidence.yaml
fibsem/applications/autolamella/protocol/legacy/protocol-liftout.yaml
fibsem/applications/autolamella/protocol/legacy/protocol-on-grid.yaml
fibsem/applications/autolamella/protocol/legacy/protocol-serial-liftout.yaml
fibsem/applications/autolamella/protocol/legacy/protocol-trench.yaml
fibsem/applications/autolamella/protocol/legacy/protocol-waffle.yaml
fibsem/applications/autolamella/tools/__init__.py
fibsem/applications/autolamella/tools/artifacts.py
fibsem/applications/autolamella/tools/data.py
fibsem/applications/autolamella/tools/experiments.py
fibsem/applications/autolamella/tools/ml_export.py
fibsem/applications/autolamella/tools/notebook.ipynb
fibsem/applications/autolamella/tools/reporting.py
fibsem/applications/autolamella/tools/stats.py
fibsem/applications/autolamella/tools/upload_to_hf.py
fibsem/applications/autolamella/ui/AutoLamellaMainUI.py
fibsem/applications/autolamella/ui/AutoLamellaUI.py
fibsem/applications/autolamella/ui/__init__.py
fibsem/applications/autolamella/ui/autolamella_apply_protocol_dialog.py
fibsem/applications/autolamella/ui/autolamella_create_experiment_widget.py
fibsem/applications/autolamella/ui/autolamella_fluorescence_acquisition_task_config_widget.py
fibsem/applications/autolamella/ui/autolamella_fluorescence_overview_tab.py
fibsem/applications/autolamella/ui/autolamella_generate_report_widget.py
fibsem/applications/autolamella/ui/autolamella_global_task_editor_dialog.py
fibsem/applications/autolamella/ui/autolamella_lamella_protocol_editor.py
fibsem/applications/autolamella/ui/autolamella_load_experiment_widget.py
fibsem/applications/autolamella/ui/autolamella_load_task_protocol_widget.py
fibsem/applications/autolamella/ui/autolamella_overview_image_widget.py
fibsem/applications/autolamella/ui/autolamella_overview_tab.py
fibsem/applications/autolamella/ui/autolamella_protocol_information_widget.py
fibsem/applications/autolamella/ui/autolamella_task_config_editor.py
fibsem/applications/autolamella/ui/autolamella_task_config_widget.py
fibsem/applications/autolamella/ui/fluorescence_coincidence_viewer_widget.py
fibsem/applications/autolamella/ui/lamella_card_widget.py
fibsem/applications/autolamella/ui/lamella_default_config_widget.py
fibsem/applications/autolamella/ui/lamella_list_widget.py
fibsem/applications/autolamella/ui/lamella_name_list_widget.py
fibsem/applications/autolamella/ui/lamella_pose_list_widget.py
fibsem/applications/autolamella/ui/lamella_task_image_widget.py
fibsem/applications/autolamella/ui/lamella_workflow_widget.py
fibsem/applications/autolamella/ui/overview_container_tab.py
fibsem/applications/autolamella/ui/overview_tab_base.py
fibsem/applications/autolamella/ui/run_ui.py
fibsem/applications/autolamella/ui/selected_lamella_widget.py
fibsem/applications/autolamella/ui/task_history_table_widget.py
fibsem/applications/autolamella/ui/workflow_config_widget.py
fibsem/applications/autolamella/ui/workflow_info_widget.py
fibsem/applications/autolamella/ui/workflow_preflight_dialog.py
fibsem/applications/autolamella/ui/workflow_task_editor_widget.py
fibsem/applications/autolamella/ui/workflow_timeline_widget.py
fibsem/applications/autolamella/ui/tests/test-lamella-card.py
fibsem/applications/autolamella/ui/tests/test-lamella-list.py
fibsem/applications/autolamella/ui/tests/test-lamella-workflow.py
fibsem/applications/autolamella/ui/tests/test-selected-lamella.py
fibsem/applications/autolamella/ui/tests/test-workflow-config.py
fibsem/applications/autolamella/ui/tests/test_coincidence_viewer_canvas.py
fibsem/applications/autolamella/ui/tests/test_confirm_run_workflow_dialog.py
fibsem/applications/autolamella/ui/tests/test_lamella_default_config_widget.py
fibsem/applications/autolamella/ui/tests/test_lamella_name_list_widget.py
fibsem/applications/autolamella/ui/tests/test_lamella_protocol_editor_canvas.py
fibsem/applications/autolamella/ui/tests/test_lamella_task_image_widget.py
fibsem/applications/autolamella/ui/tests/test_workflow_task_editor_widget.py
fibsem/applications/autolamella/ui/tests/test_workflow_timeline_animation.py
fibsem/applications/autolamella/workflows/_default_milling_config.py
fibsem/applications/autolamella/workflows/core.py
fibsem/applications/autolamella/workflows/ui.py
fibsem/applications/autolamella/workflows/workflow_estimate.py
fibsem/applications/autolamella/workflows/tasks/__init__.py
fibsem/applications/autolamella/workflows/tasks/acquire_fluorescence.py
fibsem/applications/autolamella/workflows/tasks/base.py
fibsem/applications/autolamella/workflows/tasks/basic_milling.py
fibsem/applications/autolamella/workflows/tasks/fiducial.py
fibsem/applications/autolamella/workflows/tasks/grid-task-notebook.ipynb
fibsem/applications/autolamella/workflows/tasks/grid_tasks.py
fibsem/applications/autolamella/workflows/tasks/manager.py
fibsem/applications/autolamella/workflows/tasks/mill_coincident.py
fibsem/applications/autolamella/workflows/tasks/polishing.py
fibsem/applications/autolamella/workflows/tasks/queue.py
fibsem/applications/autolamella/workflows/tasks/reference_image.py
fibsem/applications/autolamella/workflows/tasks/rough.py
fibsem/applications/autolamella/workflows/tasks/select_fluorescence_position.py
fibsem/applications/autolamella/workflows/tasks/select_position.py
fibsem/applications/autolamella/workflows/tasks/spot_burn.py
fibsem/applications/autolamella/workflows/tasks/tasks.py
fibsem/applications/autolamella/workflows/tasks/trench.py
fibsem/applications/autolamella/workflows/tasks/undercut.py
fibsem/autofunctions/__init__.py
fibsem/autofunctions/acb.py
fibsem/autofunctions/autofocus.py
fibsem/autofunctions/charge_neutralisation.py
fibsem/autofunctions/gamma.py
fibsem/autofunctions/integration.py
fibsem/autofunctions/metrics.py
fibsem/autofunctions/plotting.py
fibsem/autofunctions/stacking.py
fibsem/chat/.gitignore
fibsem/chat/main.py
fibsem/chat/requirements.txt
fibsem/config/default-sample-holder.yaml
fibsem/config/microscope-configuration.yaml
fibsem/config/odemis-configuration.yaml
fibsem/config/sample-holder.yaml
fibsem/config/sim-arctis-configuration.yaml
fibsem/config/tescan-configuration.yaml
fibsem/config/tescan_manipulator.yaml
fibsem/config/tfs-aquilos2-configuration.yaml
fibsem/config/tfs-arctis-configuration.yaml
fibsem/config/tfs-hydra-configuration.yaml
fibsem/config/fm/fm-configuration-default.yaml
fibsem/correlation/README.md
fibsem/correlation/__init__.py
fibsem/correlation/config.py
fibsem/correlation/correlation_v2.py
fibsem/correlation/fit_diagnostics.py
fibsem/correlation/history.py
fibsem/correlation/io.py
fibsem/correlation/refractive_index.py
fibsem/correlation/structures.py
fibsem/correlation/test_correlation_v2.py
fibsem/correlation/util.py
fibsem/correlation/pyto/__init__.py
fibsem/correlation/pyto/affine.py
fibsem/correlation/pyto/affine_2d.py
fibsem/correlation/pyto/attributes.py
fibsem/correlation/pyto/points.py
fibsem/correlation/pyto/rigid_3d.py
fibsem/correlation/pyto/util.py
fibsem/correlation/pyto/test/test_affine.py
fibsem/correlation/pyto/test/test_affine_2d.py
fibsem/correlation/pyto/test/test_rigid_3d.py
fibsem/correlation/tests/__init__.py
fibsem/correlation/tests/eval_lut_precision.py
fibsem/detection/__init__.py
fibsem/detection/config-autolamella-liftout-hf-mega.yaml
fibsem/detection/config-autolamella-liftout.yaml
fibsem/detection/config-autolamella-serial-liftout-hf-mega.yaml
fibsem/detection/config-autolamella-serial-liftout.yaml
fibsem/detection/config-autolamella-waffle-v2-hf-mega.yaml
fibsem/detection/config-autolamella-waffle-v2.yaml
fibsem/detection/config-autolamella-waffle.yml
fibsem/detection/config-autoliftout-dm-embryo.yml
fibsem/detection/detection.py
fibsem/detection/evaluation.py
fibsem/detection/run_evaluation.py
fibsem/detection/test_image.tif
fibsem/detection/test_image_2.tif
fibsem/detection/utils.py
fibsem/detection/test_images/test_needle_mask.tif
fibsem/detection/test_images/test_needle_mask2.tif
fibsem/detection/test_images/test_needle_mask3.tif
fibsem/detection/test_images/serial/serial_liftout_mask_00.tif
fibsem/detection/test_images/serial/serial_liftout_mask_01.tif
fibsem/detection/test_images/serial/serial_liftout_mask_02.tif
fibsem/detection/test_images/serial/serial_liftout_mask_03.tif
fibsem/detection/test_images/serial/serial_liftout_mask_04.tif
fibsem/detection/test_images/serial/serial_liftout_mask_05.tif
fibsem/detection/test_images/serial/serial_liftout_mask_06.tif
fibsem/detection/test_images/serial/serial_liftout_mask_07.tif
fibsem/fm/__init__.py
fibsem/fm/acquisition.py
fibsem/fm/autoscript.py
fibsem/fm/composite.py
fibsem/fm/config.py
fibsem/fm/fm-example-notebook.ipynb
fibsem/fm/fm-notebook.ipynb
fibsem/fm/microscope.py
fibsem/fm/odemis.py
fibsem/fm/planning.py
fibsem/fm/plot_autofocus_demo.py
fibsem/fm/preview.py
fibsem/fm/progress.py
fibsem/fm/reprojection.py
fibsem/fm/structures.py
fibsem/fm/timing.py
fibsem/fm/calibration/__init__.py
fibsem/imaging/.gitkeep
fibsem/imaging/__init__.py
fibsem/imaging/drawing.py
fibsem/imaging/masks.py
fibsem/imaging/reduce.py
fibsem/imaging/spot.py
fibsem/imaging/tiled.py
fibsem/imaging/transforms.py
fibsem/imaging/utils.py
fibsem/imaging/tests/__init__.py
fibsem/imaging/tests/test_drawing_widget.py
fibsem/imaging/tests/test_tile_order_strategies.py
fibsem/imaging/tiling/__init__.py
fibsem/imaging/tiling/geometry.py
fibsem/imaging/tiling/plotting.py
fibsem/imaging/tiling/progress.py
fibsem/imaging/tiling/reprojection.py
fibsem/microscopes/_stage.py
fibsem/microscopes/autoscript.py
fibsem/microscopes/notebook.ipynb
fibsem/microscopes/odemis_microscope.py
fibsem/microscopes/simulator.py
fibsem/microscopes/tescan.py
fibsem/microscopes/zeiss.py
fibsem/milling/__init__.py
fibsem/milling/base.py
fibsem/milling/config.py
fibsem/milling/core.py
fibsem/milling/properties.py
fibsem/milling/tasks.py
fibsem/milling/patterning/__init__.py
fibsem/milling/patterning/patterns2.py
fibsem/milling/patterning/plotting.py
fibsem/milling/patterning/utils.py
fibsem/milling/strategy/__init__.py
fibsem/milling/strategy/coincidence.py
fibsem/milling/strategy/overtilt.py
fibsem/milling/strategy/standard.py
fibsem/plugins/__init__.py
fibsem/plugins/loader.py
fibsem/plugins/report.py
fibsem/segmentation/README.md
fibsem/segmentation/__init__.py
fibsem/segmentation/_nnunet.py
fibsem/segmentation/adaptive_model.py
fibsem/segmentation/augmentation.ipynb
fibsem/segmentation/config-autolamella-mega-v4-xl.yml
fibsem/segmentation/config-autolamella-mega-v4.yml
fibsem/segmentation/config-autolamella-mega-v5.yml
fibsem/segmentation/config-autolamella-waffle4.yml
fibsem/segmentation/config.py
fibsem/segmentation/config.yml
fibsem/segmentation/dataset.py
fibsem/segmentation/example.ipynb
fibsem/segmentation/hf_segmentation_model.py
fibsem/segmentation/huggingface.ipynb
fibsem/segmentation/inference.py
fibsem/segmentation/model.py
fibsem/segmentation/nnunet_model.py
fibsem/segmentation/nnunet_model_v2.py
fibsem/segmentation/onnx_model.py
fibsem/segmentation/requirements.txt
fibsem/segmentation/sam_model.py
fibsem/segmentation/segmentation_config.yaml
fibsem/segmentation/test_image.tif
fibsem/segmentation/train.py
fibsem/segmentation/utils.py
fibsem/segmentation/docs/example_napari.png
fibsem/segmentation/docs/imgs/combined/combined.jpg
fibsem/segmentation/docs/imgs/labelled/label.tif
fibsem/segmentation/docs/imgs/raw/image.tif
fibsem/segmentation/models/.gitkeep
fibsem/server/GAPS.md
fibsem/server/README.md
fibsem/server/__init__.py
fibsem/server/client.py
fibsem/server/models.py
fibsem/server/server.py
fibsem/tools/_parser.py
fibsem/tools/beam_shift_alignment_test.py
fibsem/tools/bug_report.py
fibsem/tools/run_manipulator_calibration.py
fibsem/tools/run_split_dataset.py
fibsem/tools/telemetry.py
fibsem/ui/.gitkeep
fibsem/ui/FibsemCryoDepositionWidget.py
fibsem/ui/FibsemEmbeddedDetectionWidget.py
fibsem/ui/FibsemImageSettingsWidget.py
fibsem/ui/FibsemLabellingUI.py
fibsem/ui/FibsemManipulatorWidget.py
fibsem/ui/FibsemMinimapWidget.py
fibsem/ui/FibsemMovementWidget.py
fibsem/ui/FibsemSegmentationModelWidget.py
fibsem/ui/FibsemSpotBurnWidget.py
fibsem/ui/FibsemSystemSetupWidget.py
fibsem/ui/FibsemUI.py
fibsem/ui/__init__.py
fibsem/ui/icon.py
fibsem/ui/napari_style.py
fibsem/ui/notification_service.py
fibsem/ui/stylesheets.py
fibsem/ui/tokens.py
fibsem/ui/utils.py
fibsem/ui/correlation/__init__.py
fibsem/ui/correlation/widgets/__init__.py
fibsem/ui/correlation/widgets/coordinate_list_widget.py
fibsem/ui/correlation/widgets/correlation_canvas_widget.py
fibsem/ui/correlation/widgets/correlation_fm_canvas_widget.py
fibsem/ui/correlation/widgets/correlation_picking.py
fibsem/ui/correlation/widgets/correlation_point_overlay.py
fibsem/ui/correlation/widgets/correlation_setup_section.py
fibsem/ui/correlation/widgets/correlation_tab_widget.py
fibsem/ui/correlation/widgets/fit_confirmation_dialog.py
fibsem/ui/correlation/widgets/fm_interpolate_dialog.py
fibsem/ui/correlation/widgets/refractive_index_widget.py
fibsem/ui/correlation/widgets/test_correlation_canvas_demo.py
fibsem/ui/correlation/widgets/test_correlation_fm_canvas_demo.py
fibsem/ui/correlation/widgets/test_correlation_setup_section.py
fibsem/ui/correlation/widgets/test_correlation_tab_widget.py
fibsem/ui/fm/overview_app.py
fibsem/ui/fm/sparse_selection_app.py
fibsem/ui/fm/widgets/__init__.py
fibsem/ui/fm/widgets/autofocus_widget.py
fibsem/ui/fm/widgets/autofocus_widget_demo.py
fibsem/ui/fm/widgets/camera_widget.py
fibsem/ui/fm/widgets/channel_list_widget.py
fibsem/ui/fm/widgets/channel_settings_widget.py
fibsem/ui/fm/widgets/fm_image_viewer_widget.py
fibsem/ui/fm/widgets/fm_multi_channel_widget.py
fibsem/ui/fm/widgets/fm_overview_confirmation_dialog.py
fibsem/ui/fm/widgets/fm_overview_settings_widget.py
fibsem/ui/fm/widgets/fm_overview_widget.py
fibsem/ui/fm/widgets/fm_region_selector.py
fibsem/ui/fm/widgets/fm_sparse_selection_dialog.py
fibsem/ui/fm/widgets/fm_tile_preview.py
fibsem/ui/fm/widgets/histogram_widget.py
fibsem/ui/fm/widgets/line_plot_widget.py
fibsem/ui/fm/widgets/load_image_dialog.py
fibsem/ui/fm/widgets/minimap_plot_widget.py
fibsem/ui/fm/widgets/objective_control_widget.py
fibsem/ui/fm/widgets/test_channel_list_widget.py
fibsem/ui/fm/widgets/test_line_plot.py
fibsem/ui/fm/widgets/z_parameters_widget.py
fibsem/ui/icons/check.svg
fibsem/ui/icons/chevron_down.svg
fibsem/ui/icons/drag_handle.svg
fibsem/ui/icons/minus.svg
fibsem/ui/icons/plus.svg
fibsem/ui/napari/patterns.py
fibsem/ui/napari/properties.py
fibsem/ui/napari/utilities.py
fibsem/ui/qt/__init__.py
fibsem/ui/qt/gc.py
fibsem/ui/qt/threading.py
fibsem/ui/qtdesigner_files/FibsemManipulatorWidget.py
fibsem/ui/widgets/about_dialog.py
fibsem/ui/widgets/angle_measure.py
fibsem/ui/widgets/annotation_pin.py
fibsem/ui/widgets/beam_settings_widget.py
fibsem/ui/widgets/beam_widget.py
fibsem/ui/widgets/bug_report_widget.py
fibsem/ui/widgets/coincidence_milling_confirmation_dialog.py
fibsem/ui/widgets/connection_dialog.py
fibsem/ui/widgets/custom_widgets.py
fibsem/ui/widgets/dataframe_table_widget.py
fibsem/ui/widgets/detector_settings_widget.py
fibsem/ui/widgets/drag_distance.py
fibsem/ui/widgets/dual_beam_widget.py
fibsem/ui/widgets/fibsem_image_flow_widget.py
fibsem/ui/widgets/fibsem_overview_settings_widget.py
fibsem/ui/widgets/fluorescence_control_widget.py
fibsem/ui/widgets/form_builder.py
fibsem/ui/widgets/guided_setup_dialog.py
fibsem/ui/widgets/hook_config_widget.py
fibsem/ui/widgets/hud_ticker.py
fibsem/ui/widgets/image_settings_widget.py
fibsem/ui/widgets/microscope_config_widget.py
fibsem/ui/widgets/milling_alignment_widget.py
fibsem/ui/widgets/milling_settings_widget.py
fibsem/ui/widgets/milling_stage_list_widget.py
fibsem/ui/widgets/milling_stages_widget.py
fibsem/ui/widgets/milling_task_acquisition_settings_widget.py
fibsem/ui/widgets/milling_task_config_widget2.py
fibsem/ui/widgets/milling_task_viewer_widget.py
fibsem/ui/widgets/milling_widget.py
fibsem/ui/widgets/notifications.py
fibsem/ui/widgets/overview_acquisition_settings_widget.py
fibsem/ui/widgets/overview_confirmation_dialog.py
fibsem/ui/widgets/overview_grid_settings_widget.py
fibsem/ui/widgets/overview_list_widget.py
fibsem/ui/widgets/overview_widget.py
fibsem/ui/widgets/pattern_settings_widget.py
fibsem/ui/widgets/plugins_dialog.py
fibsem/ui/widgets/preferences_dialog.py
fibsem/ui/widgets/preflight.py
fibsem/ui/widgets/profile_line.py
fibsem/ui/widgets/progress_widget.py
fibsem/ui/widgets/radial_menu.py
fibsem/ui/widgets/reference_image_parameters_widget.py
fibsem/ui/widgets/sample_holder_widget.py
fibsem/ui/widgets/saved_position_widget.py
fibsem/ui/widgets/script_manager_dialog.py
fibsem/ui/widgets/script_menu.py
fibsem/ui/widgets/script_runner.py
fibsem/ui/widgets/spot_burn_coordinates_widget.py
fibsem/ui/widgets/strategy_settings_widget.py
fibsem/ui/widgets/task_summary_formatting.py
fibsem/ui/widgets/tile_mask_widget.py
fibsem/ui/widgets/tiled_overview_widget.py
fibsem/ui/widgets/workflow_summary_dialog.py
fibsem/ui/widgets/zoom_loupe.py
fibsem/ui/widgets/canvas/__init__.py
fibsem/ui/widgets/canvas/canvas_base.py
fibsem/ui/widgets/canvas/canvas_state.py
fibsem/ui/widgets/canvas/contrast_gamma_control.py
fibsem/ui/widgets/canvas/fm_canvas.py
fibsem/ui/widgets/canvas/fm_composite.py
fibsem/ui/widgets/canvas/image_canvas.py
fibsem/ui/widgets/canvas/overlay_controls.py
fibsem/ui/widgets/canvas/quad_view.py
fibsem/ui/widgets/canvas/real_space_canvas.py
fibsem/ui/widgets/canvas/stage_frame.py
fibsem/ui/widgets/canvas/overlays/__init__.py
fibsem/ui/widgets/canvas/overlays/alignment_overlay.py
fibsem/ui/widgets/canvas/overlays/base.py
fibsem/ui/widgets/canvas/overlays/gridbar_overlay.py
fibsem/ui/widgets/canvas/overlays/mask_overlay.py
fibsem/ui/widgets/canvas/overlays/milling_overlay.py
fibsem/ui/widgets/canvas/overlays/minimap_overlays.py
fibsem/ui/widgets/canvas/overlays/pattern_overlay.py
fibsem/ui/widgets/canvas/overlays/point_overlay.py
fibsem/ui/widgets/canvas/overlays/rect_overlay.py
fibsem/ui/widgets/canvas/overlays/ruler_overlay.py
fibsem/ui/widgets/canvas/overlays/stage_context.py
fibsem/ui/widgets/canvas/overlays/tile_grid_options_panel.py
fibsem/ui/widgets/canvas/overlays/tile_grid_overlay.py
fibsem/ui/widgets/tests/test-icon-tool-button.py
fibsem/ui/widgets/tests/test-image-settings-widget.py
fibsem/ui/widgets/tests/test-progress-bar.py
fibsem/ui/widgets/tests/test-spinner-icon.py
fibsem/ui/widgets/tests/test_active_overlay_mode.py
fibsem/ui/widgets/tests/test_alignment_comparison.py
fibsem/ui/widgets/tests/test_alignment_overlay.py
fibsem/ui/widgets/tests/test_alignment_plot_v2.py
fibsem/ui/widgets/tests/test_canvas_modifiers.py
fibsem/ui/widgets/tests/test_canvas_overlay_reducer.py
fibsem/ui/widgets/tests/test_canvas_pixel_size.py
fibsem/ui/widgets/tests/test_canvas_preserve_zoom.py
fibsem/ui/widgets/tests/test_coincidence_milling_confirmation_dialog.py
fibsem/ui/widgets/tests/test_countdown_progress.py
fibsem/ui/widgets/tests/test_detection_overlay.py
fibsem/ui/widgets/tests/test_drag_distance.py
fibsem/ui/widgets/tests/test_empty_canvas_clicks.py
fibsem/ui/widgets/tests/test_fm_canvas.py
fibsem/ui/widgets/tests/test_fm_z_slider.py
fibsem/ui/widgets/tests/test_hooks_manual.py
fibsem/ui/widgets/tests/test_milling_overlay.py
fibsem/ui/widgets/tests/test_milling_settings_widget.py
fibsem/ui/widgets/tests/test_milling_stage_list.py
fibsem/ui/widgets/tests/test_milling_stages_widget.py
fibsem/ui/widgets/tests/test_milling_task_config_widget2.py
fibsem/ui/widgets/tests/test_milling_task_viewer_widget.py
fibsem/ui/widgets/tests/test_pattern_settings_widget.py
fibsem/ui/widgets/tests/test_point_overlay_legend.py
fibsem/ui/widgets/tests/test_progress_widget.py
fibsem/ui/widgets/tests/test_quad_view.py
fibsem/ui/widgets/tests/test_radial_menu.py
fibsem/ui/widgets/tests/test_radial_ruler_demo.py
fibsem/ui/widgets/tests/test_real_space_canvas_demo.py
fibsem/ui/widgets/tests/test_reference_image_parameters_widget.py
fibsem/ui/widgets/tests/test_ruler_overlay.py
fibsem/ui/widgets/tests/test_saved_position_widget.py
fibsem/ui/widgets/tests/test_spot_burn_coordinates_widget.py
fibsem/ui/widgets/tests/test_toast.py
fibsem/util/__init__.py
fibsem/util/draw_numbers.py
fibsem/util/filename.py
scripts/.gitkeep
scripts/arctis_notebook.ipynb
scripts/compat-notebook.ipynb
scripts/convert_to_nnunet_dataset.py
scripts/convert_to_onnx.py
scripts/export_nnunet_checkpoint.py
scripts/generate_segmentation_objects.py
scripts/install.bat
scripts/install.sh
scripts/notebook.ipynb
scripts/onnx_notebook.ipynb
scripts/onnx_pred.py
scripts/run.sh
scripts/run_ui.bat
scripts/shortcut.py
scripts/stack_Arctis_Script.ipynb
scripts/test-alignment-script.py
scripts/test-autofunctions-notebook.ipynb
scripts/test_acb.py
scripts/test_autofocus.py
scripts/test_confirm_buttons.py
scripts/test_glir_gc_repro.py
scripts/test_installation.py
scripts/test_rtm_script.py
scripts/test_tiled_overview_widget.py
scripts/test_update_indicator.py
scripts/test_workflow_summary_dialog.py
tests/__init__.py
tests/conftest.py
tests/tescan-test-notebook.ipynb
tests/test_acquire.py
tests/test_acquire_image_api.py
tests/test_alignment.py
tests/test_autofocus_mode.py
tests/test_autofunctions.py
tests/test_beam_stage_projection.py
tests/test_border_stylesheet_single_source.py
tests/test_bug_report.py
tests/test_cli_connection_args.py
tests/test_cli_plugins.py
tests/test_conversions.py
tests/test_example.py
tests/test_experiment_metadata_identity.py
tests/test_field_metadata_keys.py
tests/test_filename_util.py
tests/test_grid_planning.py
tests/test_guided_setup.py
tests/test_hook_context_payload.py
tests/test_hook_event_groups.py
tests/test_hooks.py
tests/test_image_display_filter.py
tests/test_image_metadata_user.py
tests/test_image_reduction.py
tests/test_image_save_paths.py
tests/test_imaging_channel_lock.py
tests/test_import_cycles.py
tests/test_manufacturers.py
tests/test_metadata_fixtures.py
tests/test_microscope.py
tests/test_milling_time_estimates.py
tests/test_movement.py
tests/test_movement_widget_vertical_gate.py
tests/test_no_acquisition_time_gamma.py
tests/test_plugin_entry_points.py
tests/test_plugin_loader.py
tests/test_plugin_report.py
tests/test_projection_height.py
tests/test_projection_paths_agree.py
tests/test_recent_channels.py
tests/test_recent_experiments.py
tests/test_reprojection.py
tests/test_sample_holder.py
tests/test_sparse_tiles.py
tests/test_structures.py
tests/test_tescan.py
tests/test_tescan_connection_lock.py
tests/test_tescan_live_imaging.py
tests/test_tescan_milling_lifecycle.py
tests/test_tescan_movement.py
tests/test_tescan_spot_burn.py
tests/test_tiled.py
tests/test_tiled_progress.py
tests/test_tiled_progress_payload.py
tests/test_tiling_package.py
tests/test_timing.py
tests/test_ui_extra_isolation.py
tests/test_update_check.py
tests/test_user_configurations.py
tests/test_utils.py
tests/test_versioning.py
tests/test_view_corrected_movement.py
tests/test_webhook_delivery.py
tests/autolamella/__init__.py
tests/autolamella/test_abort_predicate.py
tests/autolamella/test_completed_task_accessors.py
tests/autolamella/test_completion_artifacts.py
tests/autolamella/test_example_scripts.py
tests/autolamella/test_experiment_discovery.py
tests/autolamella/test_experiment_metadata_registration.py
tests/autolamella/test_experiment_session.py
tests/autolamella/test_fluorescence_pose.py
tests/autolamella/test_hook_config_loading.py
tests/autolamella/test_hook_defaults.py
tests/autolamella/test_hook_run_context.py
tests/autolamella/test_id_serialisation.py
tests/autolamella/test_milling_angle.py
tests/autolamella/test_ml_export.py
tests/autolamella/test_objective_retract.py
tests/autolamella/test_poses.py
tests/autolamella/test_post_task_thumbnail_order.py
tests/autolamella/test_report_sections.py
tests/autolamella/test_scheduled_tasks.py
tests/autolamella/test_scripting.py
tests/autolamella/test_spot_burn.py
tests/autolamella/test_spot_burn_autofocus.py
tests/autolamella/test_status_dict_vocabulary.py
tests/autolamella/test_stop_task.py
tests/autolamella/test_structures.py
tests/autolamella/test_task_duration_estimates.py
tests/autolamella/test_task_manager_completion_hooks.py
tests/autolamella/test_task_manager_hooks.py
tests/autolamella/test_task_manager_status.py
tests/autolamella/test_task_outcome_recording.py
tests/autolamella/test_task_outputs.py
tests/autolamella/test_task_queue.py
tests/autolamella/test_tasks.py
tests/autolamella/test_thumbnail_atomic_write.py
tests/autolamella/test_workflow_context_stamping.py
tests/autolamella/test_workflow_estimate.py
tests/autolamella/test_workflow_ui_call_signatures.py
tests/correlation/__init__.py
tests/correlation/test_config.py
tests/correlation/test_correlation_canvas_widget.py
tests/correlation/test_correlation_data_integrity.py
tests/correlation/test_correlation_fm_canvas_widget.py
tests/correlation/test_correlation_picking.py
tests/correlation/test_correlation_point_overlay.py
tests/correlation/test_correlation_run_folder.py
tests/correlation/test_correlation_save_plot.py
tests/correlation/test_correlation_setup_regressions.py
tests/correlation/test_correlation_setup_section.py
tests/correlation/test_correlation_tab_widget.py
tests/correlation/test_correlation_ui_honesty.py
tests/correlation/test_default_correction_factor.py
tests/correlation/test_fit_diagnostics.py
tests/correlation/test_fit_settings_survive_image_change.py
tests/correlation/test_history.py
tests/correlation/test_image_identity.py
tests/correlation/test_image_picker.py
tests/correlation/test_interpolation.py
tests/correlation/test_microscope_coordinate_conversion.py
tests/correlation/test_pre_correction.py
tests/correlation/test_refractive_index.py
tests/correlation/test_ri_tab_input_snapshot.py
tests/correlation/test_spot_burn_seeding.py
tests/correlation/test_structures.py
tests/fixtures/metadata/README.md
tests/fixtures/metadata/demo_simulator_v4.json
tests/fixtures/metadata/demo_simulator_v5.json
tests/fixtures/metadata/extract_fixtures.py
tests/fixtures/metadata/thermo_aquilos_v3.json
tests/fixtures/metadata/thermo_arctis_compustage_v3.json
tests/fixtures/plugin/.gitignore
tests/fixtures/plugin/pyproject.toml
tests/fixtures/plugin/fibsem_test_plugin/__init__.py
tests/fixtures/plugin/fibsem_test_plugin/patterns.py
tests/fixtures/plugin/fibsem_test_plugin/strategies.py
tests/fixtures/plugin/fibsem_test_plugin/tasks.py
tests/fm/__init__.py
tests/fm/_odemis_stubs.py
tests/fm/conftest.py
tests/fm/test_acquisition.py
tests/fm/test_active_channel.py
tests/fm/test_autofocus_widget.py
tests/fm/test_calibration.py
tests/fm/test_channel_fast_path.py
tests/fm/test_composite.py
tests/fm/test_config.py
tests/fm/test_fm_autofocus.py
tests/fm/test_fm_contract.py
tests/fm/test_fm_provenance.py
tests/fm/test_objective_signal.py
tests/fm/test_odemis_driver.py
tests/fm/test_planning.py
tests/fm/test_preview.py
tests/fm/test_preview_reduction.py
tests/fm/test_progress.py
tests/fm/test_reprojection.py
tests/fm/test_routines_claim_channel.py
tests/fm/test_simulated_channel_pairs.py
tests/fm/test_simulated_shared_channel.py
tests/fm/test_structures.py
tests/milling/test_base.py
tests/milling/test_coincidence_strategy.py
tests/milling/test_core.py
tests/milling/test_pattern_to_image_pixels.py
tests/milling/test_pattern_utils.py
tests/milling/test_patterns.py
tests/milling/test_stop_event.py
tests/milling/test_tasks.py
tests/ui/test_about_dialog.py
tests/ui/test_add_to_queue.py
tests/ui/test_add_to_queue_dialog.py
tests/ui/test_beam_settings_preset.py
tests/ui/test_beam_side_move_syncs_fm_pose.py
tests/ui/test_border_stylesheet.py
tests/ui/test_canvas_base.py
tests/ui/test_channel_list_recent_menu.py
tests/ui/test_click_to_move_says_so.py
tests/ui/test_coincidence_viewer_layering.py
tests/ui/test_configuration_import.py
tests/ui/test_connection_chip.py
tests/ui/test_connection_dialog.py
tests/ui/test_connection_tab_removal.py
tests/ui/test_context_menu_action_failure.py
tests/ui/test_defect_saves_once.py
tests/ui/test_editor_microscope_reconnect.py
tests/ui/test_editor_save_debounce.py
tests/ui/test_elided_label.py
tests/ui/test_experiment_adoption_logging.py
tests/ui/test_experiment_header_button.py
tests/ui/test_experiment_panel_chrome.py
tests/ui/test_fm_acquisition_state.py
tests/ui/test_fm_control_widget_progress.py
tests/ui/test_fm_control_widget_teardown.py
tests/ui/test_fm_detail_source.py
tests/ui/test_fm_frame_projection_cache.py
tests/ui/test_fm_image_viewer.py
tests/ui/test_fm_live_indicator.py
tests/ui/test_fm_output_panel.py
tests/ui/test_fm_overview_orientation.py
tests/ui/test_fm_overview_widget.py
tests/ui/test_fm_pinned_contrast.py
tests/ui/test_fm_preview_recomposite_cost.py
tests/ui/test_fm_real_space_canvas.py
tests/ui/test_fm_region_selector.py
tests/ui/test_fm_sparse_entry_point.py
tests/ui/test_fm_sparse_selection_dialog.py
tests/ui/test_fm_tile_preview.py
tests/ui/test_focus_flash.py
tests/ui/test_form_builder.py
tests/ui/test_form_writeback.py
tests/ui/test_gui_thread_migration.py
tests/ui/test_guided_setup_dialog.py
tests/ui/test_hook_config_groups.py
tests/ui/test_instructions.py
tests/ui/test_lamella_card_layout.py
tests/ui/test_lamella_defect_sync.py
tests/ui/test_lamella_row_task_state.py
tests/ui/test_lamella_thumbnail_cost.py
tests/ui/test_main_thread_gc.py
tests/ui/test_marked_position_wins_the_click.py
tests/ui/test_milling_lockout.py
tests/ui/test_minimap_progress_payload_safety.py
tests/ui/test_movement_progress.py
tests/ui/test_napari_pattern_conversion.py
tests/ui/test_no_qt_warnings_on_workflow_load.py
tests/ui/test_objective_display_signal.py
tests/ui/test_objective_wheel_move_threading.py
tests/ui/test_overlay_content_rect.py
tests/ui/test_overview_confirmation_dialog.py
tests/ui/test_overview_container_tab.py
tests/ui/test_overview_list_widget.py
tests/ui/test_overview_tab_host.py
tests/ui/test_overview_tab_wiring.py
tests/ui/test_overview_tabs_agree.py
tests/ui/test_overview_widget.py
tests/ui/test_plugins_dialog.py
tests/ui/test_point_overlay_colour.py
tests/ui/test_position_field_of_view.py
tests/ui/test_preferences_dialog.py
tests/ui/test_progress_widget_states.py
tests/ui/test_qt_threading.py
tests/ui/test_quickstart_flags.py
tests/ui/test_real_space_canvas.py
tests/ui/test_script_manager_dialog.py
tests/ui/test_script_menu.py
tests/ui/test_script_runner.py
tests/ui/test_scripts_feature_flag.py
tests/ui/test_select_all_sync.py
tests/ui/test_selection_clearing.py
tests/ui/test_settings_widgets_integer.py
tests/ui/test_shared_palette.py
tests/ui/test_stage_frame.py
tests/ui/test_status_bar_tile_outcome.py
tests/ui/test_stylesheets_render.py
tests/ui/test_system_setup_widget.py
tests/ui/test_task_config_parameter_widgets.py
tests/ui/test_task_output_discovery.py
tests/ui/test_task_row_layout.py
tests/ui/test_task_schedule_editor.py
tests/ui/test_text_overlay.py
tests/ui/test_tile_grid_overlay.py
tests/ui/test_toast_anchoring.py
tests/ui/test_toasts_are_not_optional.py
tests/ui/test_viewer_less_widgets.py
tests/ui/test_wheel_blocker.py
tests/ui/test_workflow_poi_overlay.py
tests/ui/test_workflow_preflight_dialog.py
tests/ui/test_workflow_task_requires.py
tests/ui/test_workflow_timeline_actions.py
tests/ui/test_workflow_timeline_estimate.py
tests/ui/test_workflow_timeline_sync.py
tests/ui/test_workflow_update_payload.py