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: