Video lecture

Youtube

A video tutorial is nice to see ABBA in action, and to check the little details which may have been missed in other documentation forms. However, be aware that, while not very different, the version presented in the video tutorial is not up-to-date with this documentation.

Also, there’s no information about DeepSlice neither QuPath post-processing in the video. Here are some links with timestamps:

Youtube video tutorial (March 2022).

• Introduction and installation

• 0:00 Introduction

• 0:30 Installation

• Dataset definition, atlas display, and QuPath project import

• 1:27 Dataset presentation

• 2:25 Dataset definition in QuPath

• 4:58 Bdv navigation and Atlas display options

• 7:52 QuPath project import

• Description of ABBA’s interface

• 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

• Manual registration of sections along Z

• 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

• Saving your work

• 23:43 How to save your work (state file)

• 24:04 Closing and reopening from a state file

• In-plane registrations of the sections (manual & automated, linear & non-linear)

• 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

• Review and improve your registrations if necessary

• 35:30 Browsing registration steps

• 37:30 What you can attempt to improve the registration quality

• Export results to QuPath

• 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

Mediaspace - video without ads

A copy of this video is available in https://mediaspace.epfl.ch

Mediaspace video tutorial (March 2022).

• Introduction and installation

• 0:00 Introduction

• 0:30 Installation

• Dataset definition, atlas display, and QuPath project import

• 1:27 Dataset presentation

• 2:25 Dataset definition in QuPath

• 4:58 Bdv navigation and Atlas display options

• 7:52 QuPath project import

• Description of ABBA’s interface

• 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

• Manual registration of sections along Z

• 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

• Saving your work

• 23:43 How to save your work (state file)

• 24:04 Closing and reopening from a state file

• In-plane registrations of the sections (manual & automated, linear & non-linear)

• 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

• Review and improve your registrations if necessary

• 35:30 Browsing registration steps

• 37:30 What you can attempt to improve the registration quality

• Export results to QuPath

• 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