.gitignore
CHANGES.md
INSTALLATION.md
LICENSE
MANIFEST.in
README.md
mkdocs.yml
requirements.txt
setup.cfg
setup.py
.github/workflows/docs.yml
.github/workflows/python-package.yml
example/autolamella.py
example/example.ipynb
example/example.py
example/example_imaging.py
example/example_milling.py
example/example_movement.py
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
external/application_files/autolamella.xml
external/application_files/cryo_Pt_dep.xml
fibsem/__init__.py
fibsem/_version.py
fibsem/acquire.py
fibsem/alignment.py
fibsem/calibration.py
fibsem/config.py
fibsem/configuration.py
fibsem/constants.py
fibsem/conversions.py
fibsem/gis.py
fibsem/microscope.py
fibsem/milling.py
fibsem/movement.py
fibsem/patterning.py
fibsem/structures.py
fibsem/utils.py
fibsem/validation.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/chat/.gitignore
fibsem/chat/main.py
fibsem/chat/requirements.txt
fibsem/config/deposition.dbp
fibsem/config/microscope-configuration.yaml
fibsem/config/positions.yaml
fibsem/config/protocol.yaml
fibsem/config/tescan_manipulator.yaml
fibsem/config/user-configurations.yaml
fibsem/db/app.py
fibsem/db/config.yaml
fibsem/db/notebook.ipynb
fibsem/db/util.py
fibsem/detection/__init__.py
fibsem/detection/config-autolamella-liftout.yaml
fibsem/detection/config-autolamella-serial-liftout.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/imaging/.gitkeep
fibsem/imaging/__init__.py
fibsem/imaging/_tile.py
fibsem/imaging/autogamma.py
fibsem/imaging/masks.py
fibsem/imaging/utils.py
fibsem/segmentation/README.md
fibsem/segmentation/__init__.py
fibsem/segmentation/_nnunet.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-serial-liftout-v1.yaml
fibsem/segmentation/config-autolamella-waffle4.yml
fibsem/segmentation/config.py
fibsem/segmentation/config.yml
fibsem/segmentation/dataset.py
fibsem/segmentation/example.ipynb
fibsem/segmentation/inference.py
fibsem/segmentation/model.py
fibsem/segmentation/nnunet_model.py
fibsem/segmentation/onnx_model.py
fibsem/segmentation/requirements.txt
fibsem/segmentation/sam_model.py
fibsem/segmentation/segmentation_config.yaml
fibsem/segmentation/spacetomo_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/tools/_parser.py
fibsem/tools/run_manipulator_calibration.py
fibsem/tools/run_split_dataset.py
fibsem/tools/telemetry.py
fibsem/ui/.gitkeep
fibsem/ui/FibsemAlignmentWidget.py
fibsem/ui/FibsemCryoDepositionWidget.py
fibsem/ui/FibsemCryoDepositionWidget_qt.py
fibsem/ui/FibsemDetectionUI.py
fibsem/ui/FibsemDetectionWidget.py
fibsem/ui/FibsemEmbeddedDetectionWidget.py
fibsem/ui/FibsemFeatureLabellingUI.py
fibsem/ui/FibsemGISWidget.py
fibsem/ui/FibsemImageSettingsWidget.py
fibsem/ui/FibsemImageViewer.py
fibsem/ui/FibsemLabellingUI.py
fibsem/ui/FibsemManipulatorWidget.py
fibsem/ui/FibsemMicroscopeConfigurationWidget.py
fibsem/ui/FibsemMicroscopeConfigurationWidgetBase.py
fibsem/ui/FibsemMillingWidget.py
fibsem/ui/FibsemMinimapWidget.py
fibsem/ui/FibsemModelTrainingWidget.py
fibsem/ui/FibsemMovementWidget.py
fibsem/ui/FibsemMultiChemWidget.py
fibsem/ui/FibsemPositionsWidget.py
fibsem/ui/FibsemSegmentationModelWidget.py
fibsem/ui/FibsemSystemSetupWidget.py
fibsem/ui/FibsemUI.py
fibsem/ui/__init__.py
fibsem/ui/_stylesheets.py
fibsem/ui/utils.py
fibsem/ui/windows.py
fibsem/ui/qtdesigner_files/CurrentAlignmentWidget.py
fibsem/ui/qtdesigner_files/FibsemCryoDepositionWidget.py
fibsem/ui/qtdesigner_files/FibsemDetectionWidget.py
fibsem/ui/qtdesigner_files/FibsemEmbeddedDetectionWidget.py
fibsem/ui/qtdesigner_files/FibsemFeatureDetectionUI.py
fibsem/ui/qtdesigner_files/FibsemGISWidget.py
fibsem/ui/qtdesigner_files/FibsemLabellingUI.py
fibsem/ui/qtdesigner_files/FibsemManipulatorWidget.py
fibsem/ui/qtdesigner_files/FibsemMicroscopeConfigurationWidget.py
fibsem/ui/qtdesigner_files/FibsemMicroscopeConfigurationWidgetBase.py
fibsem/ui/qtdesigner_files/FibsemMillingWidget.py
fibsem/ui/qtdesigner_files/FibsemMinimapWidget.py
fibsem/ui/qtdesigner_files/FibsemModelTrainingWidget.py
fibsem/ui/qtdesigner_files/FibsemMovementWidget.py
fibsem/ui/qtdesigner_files/FibsemMultiChemWidget.py
fibsem/ui/qtdesigner_files/FibsemPositionsWidget.py
fibsem/ui/qtdesigner_files/FibsemSegmentationModelWidget.py
fibsem/ui/qtdesigner_files/FibsemSystemSetupWidget.py
fibsem/ui/qtdesigner_files/FibsemUI.py
fibsem/ui/qtdesigner_files/ImageSettingsWidget.py
fibsem/ui/qtdesigner_files/detection_dialog.py
fibsem/ui/qtdesigner_files/image_viewer.py
scripts/.gitkeep
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/run.sh
scripts/run_ui.bat
scripts/shortcut.py
scripts/test_installation.py
tests/test_alignment.py
tests/test_example.py
tests/test_movement.py
tests/test_structures.py