jefferislab / bridgingregistrations Goto Github PK

git on windows may check out the registration files with CRLF and CMTK doesn't like this.

@ajdm would be great if you have a mo for this.

@ajdm do you know where this came from?

IS2_Cell07 was corrected, but this transform seems odd to me.

Cell07PNs.is2=xform_brain(Cell07PNs[1:5], sample="Cell07", ref=IS2)
plot3d(Cell07PNs.is2)
plot3d(IS2)

i.e. your image with the connections between all the brains that have bridging registrations.

should be able to register to FCWB. @ajdm maybe on Thu?

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.