Help for ABBA in Fiji: Any tutorial for ABBA?

Hi,

I recently found out about the ABBA, a brain image aligner for Fiji.
I think I have installed ABBA successfully, and have loaded image onto the GUI.
But after that, I am at a loss as to how to register/align/manipulate image with so many options on the screen.
Are there any tutorial that I can utilize,
or if anyone has tried ABBA, I would gladly accept any guide or tips.

Thanks.

Dependencies

ABBA 0.1.43-SNAPSHOT-a904c6961413ddd76b9bcd8a8963cbe34badf1f6
BigWarp 6.0.3-SNAPSHOT-NOCULLING
Bdv 10.2.0
Bdv Vistools 1.0.0-beta-28
Bdv Biop Tools 0.2.4
Bdv Playground 0.2.10
Bdv BioFormats 0.2.14
Biop Wrappers 0.3.17
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A link would make it easier for others to know what you’re talking about.

I suppose you mean:

https://c4science.ch/w/bioimaging_and_optics_platform_biop/image-processing/image-to-atlas-registration/

… and the corresponding GitHub repository:

I’m tagging @NicoKiaru, the author, as he’ll certainly be able to help :slightly_smiling_face:

2 Likes

Good searching skills! The issue is that I push all publicly but it’s not released, not even beta, that’s why there’s only a very partial documentation.

Good to know! At least this part won’t need documentation :wink:

A few more weeks should do the trick hopefully. But there’s nothing yet except what @imagejan linked. And thus nothing on how to perform the registration. (I feared this part would need documentation).

I’m also glad the ‘help button’ with dependencies is working!

2 Likes

Hi,

I was wondering if those few weeks have already passed?

I also managed to install ABBA succesfully and import several images (of coronal slices) to align to the Allen Brain Atlas, furthermore I could drag the to the right position within the atlas and manage the distance between the slices.
When I switch to registration mode, however, I stumble upon a problem: I can not see the overlay between my image and the atlas, but I simply see a white rectangle. (see image below)

Could you maybe help me further or let me know when the beta version or more documentation is released?
Thank you in advance!