Register brain sections to a 3D atlas in Fiji, with ABBA 0.24.1

# Aligning Big Brains and Atlases

Register brain sections to a 3D atlas in Fiji, with ABBA 0.24.1

## In this video

- Start ABBA and open demo sections
- Position the sections along the atlas with DeepSlice
- Refine the registration in plane with Elastix
- Export the atlas regions to QuPath

Read the documentation to register your own sections, and analyse them in QuPath.

## Commands used in this video

- **ABBA Start** (v0.24.1) — https://github.com/BIOP/ijp-imagetoatlas/blob/ImageToAtlasRegister-0.24.1/src/main/java/ch/epfl/biop/atlas/aligner/gui/bdv/ABBABdvStartCommand.java
- **DeepSlice Registration** (v0.24.1) — https://github.com/BIOP/ijp-imagetoatlas/blob/ImageToAtlasRegister-0.24.1/src/main/java/ch/epfl/biop/atlas/aligner/command/RegisterSlicesDeepSliceApposeCommand.java
- **Edit Last Registration** (v0.24.1) — https://github.com/BIOP/ijp-imagetoatlas/blob/ImageToAtlasRegister-0.24.1/src/main/java/ch/epfl/biop/atlas/aligner/command/RegisterSlicesEditLastCommand.java
- **Elastix Registration (Affine)** (v0.24.1) — https://github.com/BIOP/ijp-imagetoatlas/blob/ImageToAtlasRegister-0.24.1/src/main/java/ch/epfl/biop/atlas/aligner/command/RegisterSlicesElastixAffineCommand.java
- **Elastix Registration (Spline)** (v0.24.1) — https://github.com/BIOP/ijp-imagetoatlas/blob/ImageToAtlasRegister-0.24.1/src/main/java/ch/epfl/biop/atlas/aligner/command/RegisterSlicesElastixSplineCommand.java
- **Export Slices To New QuPath Project** (v0.24.1) — https://github.com/BIOP/ijp-imagetoatlas/blob/ImageToAtlasRegister-0.24.1/src/main/java/ch/epfl/biop/atlas/aligner/command/ExportSlicesToNewQuPathProjectCommand.java
- **Open Atlas** (v0.24.1) — https://github.com/BIOP/ijp-imagetoatlas/blob/ImageToAtlasRegister-0.24.1/src/main/java/ch/epfl/biop/atlas/scijava/AtlasChooserCommand.java
- **Open Demo Slices From ZENODO** (v0.24.1) — https://github.com/BIOP/ijp-imagetoatlas/blob/ImageToAtlasRegister-0.24.1/src/main/java/ch/epfl/biop/atlas/aligner/command/ImportDemoSlicesZENODOCommand.java
- **Save State** (v0.24.1) — https://github.com/BIOP/ijp-imagetoatlas/blob/ImageToAtlasRegister-0.24.1/src/main/java/ch/epfl/biop/atlas/aligner/command/ABBAStateSaveCommand.java

## Links

- Documentation: https://abba-documentation.readthedocs.io
- Source: https://github.com/BIOP/ijp-imagetoatlas
- Questions: https://forum.image.sc/tag/abba

## Slide deck

Prefer to follow this tutorial at your own pace? A slide-deck version is also available:



## Chapters

0:00 Introduction
0:14 Start ABBA
1:47 The ABBA Window
3:25 Open the Demo Slices
3:59 Remove Unwanted Slices
4:39 Select Slices
5:24 Adjust the Display
6:28 Check the Orientation
8:14 Position Slices by Hand
9:26 Position Slices with DeepSlice
11:11 Register in Plane with Elastix
12:32 Review the Registrations
13:33 Edit a Registration with BigWarp
16:00 Save Your Work
16:26 Export to QuPath
17:20 Extra: Position the Slices by Hand
22:02 Resources & wrap-up