Question about raw expression value of targeted gene in mouse brain

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.

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. 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.