moving a nc82 stained image to JFRC2 space

[SridharJagannathan]

Hi @jefferis ,
I'm currently trying to move a nc82 stained image (3d stack) into a template space like JFRC2

As per the guidelines, I have converted the tiff to the nrrd format. However, I do not know how to get the template space given here like
cmtk reformatx --floating sample_image.nrrd template_brain.nrrd target_source.list

Do you know how to proceed with this, I also saw that there is an issue here, I would be happy to provide this as an example if you like.

My main goal is, I have another image that is from another channel of the same fly that has some dye markers, corresponding to some electrode points. I wish to transform that channel to the JFRC2 (using the registration that I will make above). Essentially then drawing an alpha shape around the points of the dye markers to understand the neuropil regions innervated by the electrodes.

[SridharJagannathan]

It seems, the template brain JFRC2.nrrd for the JFRC2 is available here: https://zenodo.org/record/10567. I will try the registration and post the result here. I also realised that the previous command was mainly for using the already made registration list. I will try and used the CMTK reg gui that you have made in FiJI and will post the results back here. Perhaps it would be useful If i can make an article on natverse website, as I think many labs would be unaware of such tools that you have made available in the past.

[SridharJagannathan]

I have managed to create a registration that let me to move the above mentioned nc82 stain image to the JFRC2 space.
Here I have overlayed (MIP), the green in nc82 image, blue in JFRC2 template. For this I used the FIJI plugin for the CMTK, and used the default parameters from 2010 Cachero, Ostrovsky et al paper and then applied the result of the warp registration onto the nc82 stain.

[SridharJagannathan]

@jefferis can you please check and tell me if this is an acceptable quality of registration? Thank you.

[jefferis]

Hi @SridharJagannathan, as you note this isn't a bridging registration question per se (bridging registrations map one template onto another) but just a standard floating to template registration. There is a range of general information on our lab wiki http://flybrain.mrc-lmb.cam.ac.uk/dokuwiki/doku.php?id=warping_manual:start. It isn't possible to tell whether a registration is acceptable from a 2D image – one would need to look at the stack to be sure – but it doesn't look too bad. In general the entry point for setting up CMTK registrations is https://github.com/jefferis/fiji-cmtk-gui as you have found. There are also many questions answered on the CMTK mailing list https://www.nitrc.org/forum/forum.php?forum_id=857