Downloading separate channels from the transgenic characterization atlas

I would like to download images from the transgenic characterization part of the atlas, so that I can compare the in situ results with reporter expression. These seem to only be available as RGB images… it seems like color deconvolution (eg in image j) will split the image but I am uncertain of how accurate this would be… thx for any insights


To help better understand what you want to do could you point to a specific image-series and tell us what type of analysis you would like to do?

Hello Lydian,

Thanks for responding.

At the moment, we are interested in the transgenic characterization of SST-IRES-cre line (Experiment 167643437).

We want to download the into image J and do cell counts of single and double-labeled SST in situ vs td tomato neurons. For that we need separate channels.

In the meantime, someone suggested that we simply transform from RGB to RBG stacks which seems to work. Not entirely sure if this is accurate though.

Thank you.