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• ABBA - Aligning Big Brains & Atlases
• How this documentation is organized
• How to cite ABBA

Installation

• Installation
  • With an AI assistant
    • Before you start
    • VS Code
    • Claude, Codex and other assistants
    • First run
    • Without a window
    • Privacy
    • If something goes wrong
  • ABBA installer
    • For you
    • For every user (Windows)
    • Without internet
    • Update, uninstall
    • Command line
  • In your Fiji
  • From Python
  • QuPath and its ABBA extension

Getting started

• Your first registration
  • 1. Start ABBA
  • 2. Open the demo slices
  • 3. Adjust the display
  • 4. Check the orientation
  • 5. Position the slices with DeepSlice
  • 6. Register the slices in plane
  • 7. Save your work
  • 8. Export the results to QuPath

User guide

• Prepare a QuPath project
  • Dataset requirements
  • Setting up a dataset of brain sections in QuPath
• Start ABBA and import slices
  • Start ABBA
  • Import slices
• The ABBA window
  • Navigate in the viewer
  • Atlas display
  • Display modes
  • The side panel cards
  • The right-click menu
  • Undo and redo
  • Mouse options
  • Log
• Select & display slices
  • Select slices
  • Display slices
  • Remove unwanted slices
  • Reorder channels
  • Slices with a white background
• Orient slices (coarse registration)
  • Rotate and flip slices
  • Manual affine registration
  • Hemi-sections: mirror slices
• Position slices along the atlas
  • Manual positioning
  • Correct the atlas slicing angles
  • Automated positioning with DeepSlice
• Refine the in-plane registration
  • Registration workflow and status indicators
  • Choosing the channels
  • Region of interest
  • Affine registration (automated)
  • Spline registration (automated)
  • BigWarp registration (manual)
  • Edit a registration
  • Remove a registration
  • Copy registrations from one slice to others
  • Browse registration steps
  • Registration workflow example
  • Adding your own registration method
• Save, load and share your work
  • Save the state of a session
  • Reopen a session
  • Share a registered dataset: the standardized zip
• Export results
  • Principle
  • Export to QuPath
  • Warp slices onto the atlas
  • Export the atlas coordinates of the original slices
  • Export atlas regions as ImageJ ROIs
  • Export to BigDataViewer
  • Export as a QuickNII dataset
  • Export a standardized, self-contained zip
• Analyse in QuPath
  • Give a try to BraiAn
  • Exporting ABBA registration results
  • Importing ABBA registration results: creating Atlas regions as QuPath annotations
  • Importing ABBA registration results: adding Atlas coordinates to QuPath detections measurements
  • Analysis in QuPath
  • Display results in 3D

See also

• Whole-brain analysis with BraiAn

Reference

• Menu reference
  • File
  • Edit
  • Import
  • View
  • Slices
  • Register
  • Export
  • Help
  • Cite
• Keyboard & mouse shortcuts
  • Viewer navigation
  • Slice selection
  • Editing
  • Registrations
  • Other
  • BigWarp
• Supported file formats
  • 1. Any Bio-Formats supported file format,
  • 2. ideally multi-resolution (Bio-Formats supported),
  • 3. and calibrated.
  • Tested file formats
  • More technicalities
• State & transform files
  • ABBA state files
  • How transformations are saved with JSON

Cite

• Cite ABBA
  • How to cite ABBA
  • Acknowledgements
  • Methods writing assistant
  • Citing third-party tools

Help

• Known issues & frequently asked questions
  • All ABBA related questions on forum.image.sc
  • Sections are gigantic when opened in ABBA
  • I only have hemi-brain sections. Can I use ABBA ?
  • I can’t start any elastix or DeepSlice registration
  • I cannot see any image after I import my QuPath project
  • I want to use another atlas than the ones available
  • I can’t open my state file anymore

Other resources

• Demo dataset
  • Dataset 1, provided by Lucie Dixsaut, Johannes Gräff lab, EPFL
  • Dataset 2, provided by Bianca A. Silva, Johannes Gräff lab, EPFL
• Video tutorial
  • ABBA 0.24.1
  • Video lecture (March 2022)
• Slides
  • Workshop slides (previous version)