Aligning Serial Brain Sections to the Allen Brain Atlas with ABBA

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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/

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Aligning Serial Brain Sections to the Allen Brain Atlas with ABBA

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