I’m wondering if anyone knows of tools/software that make it possible to register images of mouse spinal cord sections to the Allen Brain Atlas (or another atlas). I mostly just want to be able to differentiate white matter from grey matter, so it wouldn’t have to be super precise registration.
Thanks!
Hello Kelsey
We do not provide any specific tools to register spinal cord images to the spinal cord reference atlases. There are a plethora of tools to do image based registration. The right one for you depends on many different factors specific to your background, resources and project goals.
In general, there are two main strategies for doing image registration:
Image-based. Some version of cross-correlation and searching.
Feature-based. point match between images and solve for a transform by least squares or some iterative method.
Lots of different tools are available. A very short list is here:
Matlab https://www.mathworks.com/discovery/image-registration.html
Python: http://pyimreg.github.io/
JBA (https://github.com/Vaa3D/vaa3d_tools/tree/master/released_plugins/v3d_plugins/jba)
ANTS (http://stnava.github.io/ANTs/)
FSL (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki)
CMTK (https://www.nitrc.org/projects/cmtk)
Best regards and good luck with your project.
Wayne
Hi Kelsey,
Apart from registering sc images in two databases, you might be able to get some of the information you need by searching for white and gray matter within each atlas. For example, you could use the Browse Expression Category tool on the home page of the Mouse Spinal Cord atlas to search for all sections manually curated to have Gray Matter or White Matter.
Ralph