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• ABBA - Aligning Big Brains & Atlases
• How to cite ABBA

Installation

• Installation
  • ABBA plugin for Fiji
    • Method 1 - Windows installer
    • Method 2 - Fiji plugin manager
    • Method 3 - Installing ABBA plugin in python
  • ABBA extension for QuPath
    • QuPath 0.6
    • QuPath 0.5 (legacy - no bug fix)

How-to

• Creating a compatible QuPath project
  • Dataset requirements
    • Supported Image Formats
  • Setting up a dataset of brain sections in QuPath
• Data import & navigation
  • Navigating ABBA’s BigDataViewer
  • Atlas display options
  • Importing a QuPath Project into ABBA
  • Other import methods
    • Importing the Current ImageJ Window
    • Direct file import of a file
    • Importing from BigDataViewer Playground
• Slices selection and display
  • Selecting slices
    • Rectangle Selection with the Mouse
    • Slice display table
  • Slices display options
    • Removing Unwanted Slices
    • Displaying Specific Channels
• Registration workflow
  • Flip and/or rotate slices
  • Manual interactive transformation of slices (Scale, Translate, Rotate)
  • Slices registration | Z Axis (manual)
    • Drag selected slices
    • Distribute spacing between selected slices
    • Manual positioning along the Atlas axis + Locking Key Slices
    • Using the review mode to investigate the position of slices along the atlas
  • Correcting atlas slicing orientation
  • Slices registration | Z Axis (automated with DeepSlice)
    • Using DeepSlice web interface in ABBA
    • Using DeepSlice locally in ABBA
  • Slices registration | XY-Axis
    • Registration Workflow and Status Indicators
    • Affine registration (Automated)
    • Spline registration (Automated)
    • BigWarp registration (Manual)
    • Editing a registration
    • Browsing registration steps
  • Development - adding a registration method of your own
  • Registration workflow example
• Saving & loading states
• Exporting registration results
  • Principle
  • 1. Warping slices onto the atlas
    • Why it is not so obvious
    • Export warped slices
  • 2. Warping atlas onto the slice
  • 3. Export an image of the atlas coordinates onto the slice
  • 4. Export atlas regions in the Roi Manager
• Image analysis in QuPath
  • Give a try to BraiAn
  • Exporting ABBA registration results
  • Importing ABBA registration results: creating Atlas regions as QuPath annotations
    • Display tips
    • Automating the import for all slices
  • Importing ABBA registration results: adding Atlas coordinates to QuPath detections measurements
    • Allen Brain CCFv3 coordinates
  • Analysis in QuPath
    • Basic QuPath scripts
  • Display results in 3D

See also

• Whole-brain analysis with BraiAn

Tutorial

• Demo dataset
  • Dataset 1, provided by Lucie Dixsaut, Johannes Gräff lab, EPFL
  • Dataset 2, provided by Bianca A. Silva, Johannes Gräff lab, EPFL
• Video lecture
  • Youtube
  • Mediaspace - video without ads
• Slides

Advanced

• Supported data sources
  • 1. Any Bio-Formats supported file format,
  • 2. ideally multi-resolution (Bio-Formats supported),
  • 3. and calibrated.
  • Tested file formats
  • More technicalities
• Specification: save state & exported files
  • ABBA state files
    • File(s) _bdvdataset_{i}.xml
    • File sources.json
    • File state.json
  • How transformations are saved with JSON

FAQ

• 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 registrations
  • 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