Aligning Serial Brain Sections to the Allen Brain Atlas with ABBA

This video describes how to use ABBA to align serial brain sections to a 3D atlas. ABBA requires ImageJ/Fiji and QuPath. For a correct pace, do not hesitate to watch at 1.5x speed! (Vocab : slice = section)

0:00 Introduction
0:30 Installation
1:27 Dataset presentation
2:25 Dataset definition in QuPath
4:58 Bdv navigation and Atlas display options
7:52 QuPath project import
9:06 Short description of ABBA's interface (Bdv view, table view)
9:56 How to display the sections + how to remove unwanted sections
13:46 Selecting sections in the Bdv view
15:20 Translating sections along the Z atlas axis (antero-posterior position)
16:05 Tip: reversing section order
17:14 How to cancel an action
17:38 First key slice
19:19 Second key slice (+atlas cutting angle adjustment)
21:54 Third key slice
23:00 Distribute spacing between sections
23:43 How to save your work (state file)
24:04 Closing and reopening from a state file
24:51 Introducing positioning and review modes
26:00 Browsing sections in review mode
27:15 Manual affine in-plane registration
29:50 Automated affine in-plane registration
33:28 Automated spline in-plane registration
35:30 Browsing registration steps
37:30 What you can attempt to improve the registration quality
39:29 Export registration results from Fiji to QuPath
40:04 Import registration results in QuPath
42:14 How to correct a registration result with BigWarp
46:42 Conclusion

Links from the video:
installation : https://go.epfl.ch/abba-install
complete documentation : https://go.epfl.ch/abba
dataset : https://zenodo.org/record/5018719#.Yp... (1 zip with all files)
dataset : https://zenodo.org/record/6553641#.Yp... (1 zip per file)
forum image sc : https://forum.image.sc/