# Question about raw expression value of targeted gene in mouse brain

**URL:** <https://community.brain-map.org/t/question-about-raw-expression-value-of-targeted-gene-in-mouse-brain/1202>\
**Category:** Science\
**Tags:** atlas-mouse-brain-adult, analysis\
**Created:** [July 23, 2021, 8:35am UTC](https://community.brain-map.org/t/question-about-raw-expression-value-of-targeted-gene-in-mouse-brain/1202 "2021-07-23T08:35:48Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![sttmfgml63](https://avatars.discourse-cdn.com/v4/letter/s/90db22/32.png) [@sttmfgml63](https://community.brain-map.org/u/sttmfgml63)\
**Post date:** [July 23, 2021, 8:35am UTC](https://community.brain-map.org/t/question-about-raw-expression-value-of-targeted-gene-in-mouse-brain/1202/1 "2021-07-23T08:35:48Z")

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Hello, allen institute.

I’m writing to inquire a question about the raw expression value of targeted gene that was indicated in ISH data of Allen Brain Atlas : mouse brain. I know the value of structure A is expression energy, but I can’t understand it. I wonder how raw expression value was caculated deeply.

In fact, I want to convert raw expression value to TPM. If you know how to do that, please teach me with detailed example.

I will looking for your team’s response.

Thank you.

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**Author:** ![jeremyinseattle](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/jeremyinseattle/32/50_2.png) [@jeremyinseattle](https://community.brain-map.org/u/jeremyinseattle)\
**Post date:** [July 23, 2021, 4:08pm UTC](https://community.brain-map.org/t/question-about-raw-expression-value-of-targeted-gene-in-mouse-brain/1202/2 "2021-07-23T16:08:52Z")

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Hi @sttmfgml63! ISH is a semi-quantitative metric and therefore cannot be directly converted to TPM. One way of measuring gene expression is the expression energy, which is a calculated metric described in more detail [in the help documentation](http://help.brain-map.org/display/mousebrain/In+Situ+Hybridization+%28ISH%29+Data#InSituHybridization(ISH)Data-ExpressionEnergy). In part: “The Expression Energy was calculated as follows: Within a given area A (voxel or structure), expression energy = (sum of intensity of expressing pixels in A) / (sum of all pixels in A).” Others at the Allen Institute could provide additional details if needed.