.gitignore
CITATION.md
LICENSE
README.md
changes.md
install.bat
mkdocs.yml
pyproject.toml
requirements.txt
setup.cfg
setup.py
shortcut.py
ui.bat
.github/workflows/docs.yml
autolamella/__init__.py
autolamella/_version.py
autolamella/config.py
autolamella/notebook.ipynb
autolamella/structures.py
autolamella/system.yaml
autolamella/utils.py
autolamella/waffle.py
autolamella.egg-info/PKG-INFO
autolamella.egg-info/SOURCES.txt
autolamella.egg-info/dependency_links.txt
autolamella.egg-info/entry_points.txt
autolamella.egg-info/requires.txt
autolamella.egg-info/top_level.txt
autolamella/liftout/__init__.py
autolamella/liftout/actions.py
autolamella/liftout/autoliftout.py
autolamella/liftout/structures.py
autolamella/liftout/config/__init__.py
autolamella/liftout/config/config.py
autolamella/liftout/config/system.yaml
autolamella/liftout/protocol/config.yaml
autolamella/liftout/protocol/protocol.yaml
autolamella/liftout/protocol/protocol2.yaml
autolamella/liftout/protocol/protocol_auto.yaml
autolamella/liftout/protocol/protocol_serial.yaml
autolamella/liftout/protocol/protocol_yeast.yaml
autolamella/liftout/ui/AutoLiftoutUIv2.py
autolamella/liftout/ui/README.md
autolamella/liftout/ui/__init__.py
autolamella/liftout/ui/utils.py
autolamella/liftout/ui/qt/AutoLiftoutUIv2.py
autolamella/liftout/ui/qt/AutoLiftoutUIv2.ui
autolamella/liftout/ui/qt/__init__.py
autolamella/liftout/workflows/notebook.ipynb
autolamella/liftout/workflows/serial.py
autolamella/log/.gitkeep
autolamella/protocol/.gitkeep
autolamella/protocol/protocol-base.yaml
autolamella/protocol/protocol-chromatin.yaml
autolamella/protocol/protocol-waffle.yaml
autolamella/protocol/protocol.yaml
autolamella/tools/__init__.py
autolamella/tools/_parser.py
autolamella/tools/data.py
autolamella/tools/notebook.ipynb
autolamella/tools/stats.py
autolamella/tools/telemetry.py
autolamella/ui/AutoLamellaUI.py
autolamella/ui/UI.py
autolamella/ui/UI.ui
autolamella/ui/__init__.py
autolamella/ui/_stylesheets.py
autolamella/ui/utils.py
autolamella/ui/qt/AutoLamellaUI.py
autolamella/ui/qt/AutoLamellaUI.ui
autolamella/workflows/core.py
autolamella/workflows/ui.py
docs/Autolamella_test_checklist.md
docs/INSTALLATION.md
docs/extras.md
docs/features.md
docs/index.md
docs/protocol.md
docs/walkthrough.md
docs/img/NewProtocolFormat.bmp
docs/img/protocol.png
docs/img/ui.png
docs/img/ui_new.png
docs/img/features/minimap_run.png
docs/img/features/overview-ion-positions.png
docs/img/features/tools_menu.png
docs/img/features/tools_menu.png~
docs/img/walkthrough/connectToMicroscope.png
docs/img/walkthrough/connectToMicroscope2.png
docs/img/walkthrough/createExperiment.png
docs/img/walkthrough/experimentName.png
docs/img/walkthrough/experimentNmae.png
docs/img/walkthrough/experimentOverview.png
docs/img/walkthrough/lamellahistory.png
docs/img/walkthrough/lamellaoverview.png
docs/img/walkthrough/moveStage.png
docs/img/walkthrough/movingPatterns.png
docs/img/walkthrough/protoTab.png
docs/img/walkthrough/selectExperimentFolderYaml.png
docs/img/walkthrough/showLamellaAndMicroexpansionJoints.png
docs/img/walkthrough/stageanalytics.png
docs/img/walkthrough/stepsduration.png
docs/img/walkthrough/takeReferenceImages.png
docs/img/walkthrough/timeline.png
docs/img/walkthrough_2/Screenshot from 2023-08-04 11-17-32.png~
docs/img/walkthrough_2/acquire_images.png
docs/img/walkthrough_2/add_lamella.png
docs/img/walkthrough_2/add_lamella.png~
docs/img/walkthrough_2/change_protocol.png
docs/img/walkthrough_2/connect_to_microscope.png
docs/img/walkthrough_2/default_method_setup.png
docs/img/walkthrough_2/detection_ex.png
docs/img/walkthrough_2/detection_ex.png~
docs/img/walkthrough_2/finish_default.png
docs/img/walkthrough_2/finish_default.png~
docs/img/walkthrough_2/lamella_failed.png
docs/img/walkthrough_2/lamella_failed.png~
docs/img/walkthrough_2/movement_tab.png
docs/img/walkthrough_2/run_milling_default.png
docs/img/walkthrough_2/run_milling_default.png~
docs/img/walkthrough_2/run_trench_waffle.png
docs/img/walkthrough_2/run_trench_waffle.png~
docs/img/walkthrough_2/setup_default_lamella.png
docs/img/walkthrough_2/setup_default_lamella.png~
docs/img/walkthrough_2/supervision.png
docs/img/walkthrough_2/supervision.png~
scripts/.gitkeep