LICENSE
README.md
pyproject.toml
src/abba_mcp/__init__.py
src/abba_mcp/__main__.py
src/abba_mcp/fiji_tools.json
src/abba_mcp.egg-info/PKG-INFO
src/abba_mcp.egg-info/SOURCES.txt
src/abba_mcp.egg-info/dependency_links.txt
src/abba_mcp.egg-info/entry_points.txt
src/abba_mcp.egg-info/requires.txt
src/abba_mcp.egg-info/top_level.txt
src/abba_mcp/data/environment.md
src/abba_mcp/data/instructions.md
src/abba_mcp/data/commands/INDEX.md
src/abba_mcp/data/commands/Align/ABBA - BigWarp Registration.md
src/abba_mcp/data/commands/Align/ABBA - Copy and Apply Registration.md
src/abba_mcp/data/commands/Align/ABBA - DeepSlice Registration.md
src/abba_mcp/data/commands/Align/ABBA - Edit Last Registration.md
src/abba_mcp/data/commands/Align/ABBA - Elastix Registration (Affine).md
src/abba_mcp/data/commands/Align/ABBA - Elastix Registration (Spline).md
src/abba_mcp/data/commands/Align/ABBA - Manual Affine Registration.md
src/abba_mcp/data/commands/Align/ABBA - Mirror Slices.md
src/abba_mcp/data/commands/Align/ABBA - Re-index channels of slices.md
src/abba_mcp/data/commands/Align/ABBA - Remove Last Registration.md
src/abba_mcp/data/commands/Align/ABBA - Un-Mirror Slices.md
src/abba_mcp/data/commands/Atlas/ABBA - ABBA Start (alpha).md
src/abba_mcp/data/commands/Atlas/ABBA - ABBA Start.md
src/abba_mcp/data/commands/Atlas/ABBA - Align Big Brains and Atlases (no GUI).md
src/abba_mcp/data/commands/Atlas/ABBA - Close session.md
src/abba_mcp/data/commands/Atlas/ABBA - Start Logging.md
src/abba_mcp/data/commands/Atlas/Create Atlas from Images.md
src/abba_mcp/data/commands/Atlas/List BrainGlobe Atlases.md
src/abba_mcp/data/commands/Atlas/Open Atlas.md
src/abba_mcp/data/commands/Cite/ABBA - Get Prompt for Methods Writing.md
src/abba_mcp/data/commands/Cite/ABBA - How to cite.md
src/abba_mcp/data/commands/DeepSlice/DeepSlice Info.md
src/abba_mcp/data/commands/Edit/ABBA - Auto Display Range.md
src/abba_mcp/data/commands/Edit/ABBA - Delete Slices.md
src/abba_mcp/data/commands/Edit/ABBA - Deselect Slices.md
src/abba_mcp/data/commands/Edit/ABBA - Distribute Slices.md
src/abba_mcp/data/commands/Edit/ABBA - Move Slices.md
src/abba_mcp/data/commands/Edit/ABBA - Raster and cache deformation field.md
src/abba_mcp/data/commands/Edit/ABBA - Raster slice.md
src/abba_mcp/data/commands/Edit/ABBA - Rotate.md
src/abba_mcp/data/commands/Edit/ABBA - Select Slices.md
src/abba_mcp/data/commands/Edit/ABBA - Set Atlas Slicing Angles.md
src/abba_mcp/data/commands/Edit/ABBA - Set Key Slices.md
src/abba_mcp/data/commands/Edit/ABBA - Set Region Of Interest.md
src/abba_mcp/data/commands/Edit/ABBA - Set Slice Background.md
src/abba_mcp/data/commands/Edit/ABBA - Set Slices Min Max Display Range.md
src/abba_mcp/data/commands/Edit/ABBA - Set Slices Thickness (fill gaps).md
src/abba_mcp/data/commands/Edit/ABBA - Set Slices Thickness.md
src/abba_mcp/data/commands/Edit/ABBA - Undo or Redo.md
src/abba_mcp/data/commands/Export/ABBA - Export Atlas Coordinates of Original Slices to ImageJ.md
src/abba_mcp/data/commands/Export/ABBA - Export Atlas to ImageJ.md
src/abba_mcp/data/commands/Export/ABBA - Export Original Slices to ImageJ.md
src/abba_mcp/data/commands/Export/ABBA - Export Regions To File.md
src/abba_mcp/data/commands/Export/ABBA - Export Regions To Roi Manager.md
src/abba_mcp/data/commands/Export/ABBA - Export Registered Slices to BDV Json Dataset (Experimental).md
src/abba_mcp/data/commands/Export/ABBA - Export Registered Slices to BDV.md
src/abba_mcp/data/commands/Export/ABBA - Export Registered Slices to ImageJ.md
src/abba_mcp/data/commands/Export/ABBA - Export Registrations To QuPath Project.md
src/abba_mcp/data/commands/Export/ABBA - Export Resampled Slices as BDV Source ( experimental ).md
src/abba_mcp/data/commands/Export/ABBA - Export Slices To New QuPath Project.md
src/abba_mcp/data/commands/Export/ABBA - Export Standardized ABBA Project (Zip).md
src/abba_mcp/data/commands/Export/ABBA - Export registered slices as QuickNII dataset.md
src/abba_mcp/data/commands/File/ABBA - Load State.md
src/abba_mcp/data/commands/File/ABBA - Save State.md
src/abba_mcp/data/commands/Help/ABBA - Ask for help in the forum.md
src/abba_mcp/data/commands/Help/ABBA - Check for updates.md
src/abba_mcp/data/commands/Help/ABBA - Give your feedback.md
src/abba_mcp/data/commands/Help/ABBA - Go to documentation.md
src/abba_mcp/data/commands/Import/ABBA - Import Current ImageJ Window.md
src/abba_mcp/data/commands/Import/ABBA - Import QuPath Project.md
src/abba_mcp/data/commands/Import/ABBA - Import QuickNII Project.md
src/abba_mcp/data/commands/Import/ABBA - Import Sources.md
src/abba_mcp/data/commands/Import/ABBA - Import Standardized ABBA Project (Zip).md
src/abba_mcp/data/commands/Import/ABBA - Import With Bio-Formats.md
src/abba_mcp/data/commands/Inspect/ABBA - Get State.md
src/abba_mcp/data/commands/Inspect/ABBA - Snapshot.md
src/abba_mcp/data/commands/Inspect/ABBA - Wait.md
src/abba_mcp/data/commands/Multi Image To Atlas/ABBA - Adjust Slicing.md
src/abba_mcp/data/commands/Multi Image To Atlas/ABBA - Define Rectangular ROI.md
src/abba_mcp/data/commands/Multi Image To Atlas/ABBA - Open Demo Slices From OMERO.md
src/abba_mcp/data/commands/Multi Image To Atlas/ABBA - Open Demo Slices From ZENODO.md
src/abba_mcp/data/commands/Multi Image To Atlas/ABBA - Preferences.md
src/abba_mcp/data/commands/Multi Image To Atlas/ABBA - Run Benchmark.md
src/abba_mcp/data/commands/Obsolete/ABBA - DeepSlice Registration (Local).md
src/abba_mcp/data/commands/Obsolete/ABBA - DeepSlice Registration (Web).md
src/abba_mcp/data/commands/_no_menu/AllenBrainAdultMouseAtlasCCF2017Command.md
src/abba_mcp/data/commands/_no_menu/AllenBrainAdultMouseAtlasCCF2017v3p1ASRCommand.md
src/abba_mcp/data/commands/_no_menu/AllenBrainAdultMouseAtlasCCF2017v3p1Command.md
src/abba_mcp/data/commands/_no_menu/AtlasAdjustDisplayCommand.md
src/abba_mcp/data/commands/_no_menu/DisplaySettingsCommand.md
src/abba_mcp/data/commands/_no_menu/WaxholmSpragueDawleyRatV4Command.md
src/abba_mcp/data/commands/_no_menu/WaxholmSpragueDawleyRatV4p2ASRCommand.md
src/abba_mcp/data/commands/_no_menu/WaxholmSpragueDawleyRatV4p2Command.md
src/abba_mcp/data/examples/abba_demo_pipeline.groovy
src/abba_mcp/data/guides/abba.md
src/abba_mcp/data/guides/images-and-import.md
src/abba_mcp/data/guides/storage-and-exports.md
src/abba_mcp/data/guides/window.md
src/abba_mcp/data/scripting/groovy-steps.md
src/abba_mcp/data/scripting/window_picture.groovy
src/abba_mcp/data/scripting/window_view.groovy
src/abba_mcp/env/jgo.toml
src/abba_mcp/env/logback.xml
src/abba_mcp/env/startmcp.groovy