Allen Mouse ISH Expression Images question

Hi there!

I’m using the Allen mouse ISH database for a project on spatial analyses of gene expression in the mouse brain. I only recently found the “Expression” Image viewer. I’ve tried searching the white papers for more information about how these images are generated and what the colour scale represents. Is there a piece of documentation available that explains how these images are generated? I’ve included a screenshot of the “Expression” type images here, because (now I could be wrong about this), they are different from “Expression Energy.”

Any assistance is greatly appreciated, thank you :slight_smile:

Hello @MPanday, please see the documentation titled “Informatics Data Processing” at this link Documentation - Allen Mouse Brain Atlas and this paper Genome-wide atlas of gene expression in the adult mouse brain | Nature for more information on the “expression mask.”

Hi @racheld thanks for pointing me to that, I appreciate it. Another quick follow up question - is there a way to obtain the quantification data (i.e., a csv file perhaps of the individual cell quantification data for a particular image)? I know there’s a jupyter notebook for image retrieval, is there something similar to retrieve the expression quantification data?

@MPanday check out this post that can point you in the right direction. Downloading ISH or Expression data

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