Quantification of gene expression by in situ hybridization: finding and using the raw values

Many of the histological datasets that have been developed by the Allen Institute display gene expression by in situ hybridization (ISH), using colorimetric detection of RNA transcripts. Detailed methods describing how these experiments and analyses were performed are available in Technical Whitepapers that are customized to each dataset; some of those are listed below for reference.

People often want to use ‘raw’ expression values, or computed numbers that are generated as part of the analysis for visualization of data. The ISH process is only semi-quantitative due to signal amplification, so people who choose to use this information should be aware of that caveat and proceed with their analysis accordingly. Data quantification is sometimes presented as heatmaps, specifically to draw attention to the fact that these values are guides rather than absolute quantitative ‘truths’ reflecting transcript abundance.

That said, the ‘raw’ values are still useful and are available through the API, if they are not listed directly on the web page corresponding to an experiment.

For example, if you are interested in accessing raw expression values shown in this type of image from the Allen Developing Mouse Brain Atlas, you can find instructions on how to access this data through the API: http://help.brain-map.org/display/devmouse/API. There is a lot of useful information here, but the section on Structure Unionization provides information on how to access and download raw values that are calculated for a given gene of interest.

The API is a great way to dig into the data programmatically, and together with the Technical Documentation (we also call these whitepapers), you can learn so much more than by looking at the data images alone!

Technical Documents for:

We have also received several questions about how to perform structure unionization and return the output for more than one gene at a time (along with associated gene symbols). The API call below shows an example for how to do this for the genes Fam84b, Fam184a, and Rasa and return the results in json format. Several online json to csv conversion tools are available (via a Google search) if you are uncomfortable with this format.


I am trying to get the raw ISH expression values for a group of genes throughout development. The Manual Annotation give values that were annotated or predicted by down or up walks. I would like to use values that were actually annotated.
The “comments” column says whether it is an up or down walk annotation.
If the comment is blank (does not say anything), does it mean that that structures was actually manually annotated and not predicted?
Thank you

Hello Juan - that should be correct - if comment is blank it was directly annotated.