Image Registration for Expression Mask Analysis in 2D Slices


thanks for the great data and tools!

I am currently trying to create an expression dataset using ISH data from the whole mouse brain. I saw some posts in the forum regarding similar topics but i am a bit confused so I wanted to ask again.

I want to create a number of common frame slices (e.g ~20 from sagittal atlas), and register all of the sections from all gene experiments to this space. Basically at the end, I would have a data with the format of (n, x, y, g) where n is the number of slices (e.g 20), x, y as the width and height and g as the number of genes (20k) which would be the values from expression mask for example. This doesn’t have to be in a 3D voxel structure, but just different genes are expressed in a common 2D slice.

I tried to do this by using the image sync api to register the slices to the atlas frames, however, single pixel api calls takes long of course for big images and many genes. So my question is: Am I approaching this the wrong way?

Another option would be directly to get a 3D voxel grid as in the grid service for every gene but in a resolution such as 10 or 25. But as far as I understand, this is not available/not possible to do?

Thank you very much in advance!

Hi @enessenel,

For the ISH data, 3D voxel data is available at 200 micron resolution.

Example API call can be found here: