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.

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

Slide deck

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

<add slide-deck URL here once hosted>

Links

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

Commands used in this video

• ABBA Start (v0.24.1)
• DeepSlice Registration (v0.24.1)
• Edit Last Registration (v0.24.1)
• Elastix Registration (Affine) (v0.24.1)
• Elastix Registration (Spline) (v0.24.1)
• Export Slices To New QuPath Project (v0.24.1)
• Open Atlas (v0.24.1)
• Open Demo Slices From ZENODO (v0.24.1)
• Save State (v0.24.1)