# Allen Mouse ISH Expression Images question

**URL:** <https://community.brain-map.org/t/allen-mouse-ish-expression-images-question/2629>\
**Category:** Brain Knowledge Platform\
**Created:** [October 13, 2023, 2:36pm UTC](https://community.brain-map.org/t/allen-mouse-ish-expression-images-question/2629 "2023-10-13T14:36:04Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![MPanday](https://avatars.discourse-cdn.com/v4/letter/m/49beb7/32.png) [@MPanday](https://community.brain-map.org/u/MPanday)\
**Post date:** [October 13, 2023, 2:36pm UTC](https://community.brain-map.org/t/allen-mouse-ish-expression-images-question/2629/1 "2023-10-13T14:36:04Z")

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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 🙂

 ![Screenshot 2023-10-13 103302](https://canada1.discourse-cdn.com/flex027/uploads/brainobservatory/original/1X/44b57a1ebf4c3c66bb7ba8721e21d9bb872b2f6f.jpeg)

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**Author:** ![racheld](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/racheld/32/107_2.png) [@racheld](https://community.brain-map.org/u/racheld)\
**Post date:** [October 17, 2023, 10:20pm UTC](https://community.brain-map.org/t/allen-mouse-ish-expression-images-question/2629/2 "2023-10-17T22:20:16Z")

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Hello @MPanday, please see the documentation titled “Informatics Data Processing” at this link [Documentation - Allen Mouse Brain Atlas](http://help.brain-map.org/display/mousebrain/Documentation) and this paper [Genome-wide atlas of gene expression in the adult mouse brain | Nature](https://doi.org/10.1038/nature05453) for more information on the “expression mask.”

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**Author:** ![MPanday](https://avatars.discourse-cdn.com/v4/letter/m/49beb7/32.png) [@MPanday](https://community.brain-map.org/u/MPanday)\
**Post date:** [October 18, 2023, 1:27pm UTC](https://community.brain-map.org/t/allen-mouse-ish-expression-images-question/2629/3 "2023-10-18T13:27:53Z")

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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?

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**Author:** ![racheld](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/racheld/32/107_2.png) [@racheld](https://community.brain-map.org/u/racheld)\
**Post date:** [October 18, 2023, 3:21pm UTC](https://community.brain-map.org/t/allen-mouse-ish-expression-images-question/2629/4 "2023-10-18T15:21:22Z")

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@MPanday check out this post that can point you in the right direction. [Downloading ISH or Expression data](https://community.brain-map.org/t/downloading-ish-or-expression-data/376/)