I want to download the data for all available genes in the developing mouse brain dataset, across all time-points, mapped to the highest level/coarsest Structure Unionization level (i.e neuroanatomical region). The examples in the API for, e.g. Structure Unionization don’t work, and I’m unsure how …

Hi, This is probably going to be a longer answer than you expected. I’ve put together some python code (end of this post) that will, I think, do what you are asking. That being said, there’s a lot of freedom in this system, so I’m going to try to describe my process so that you can tweak the code s…

It gets 1221 genes, not 2,000. Is this an error, or does the developing atlas have only 1.2k?

I tried changing the code to get gene expression for all the genes (± region), but it seems to be looking at millions of rows now and to be very slow. Is there a better structural organization I can use , or even getting expression across the whole brain? I want as many genes as possible + temporal …

Ideally, I’d have the data in a csv, with the shape: gene_acronym,gene_name,gene_entrez_id,age,age_in_days,,structure_acronym,structure_name,expression_energy And possibly adding another column, identifying the specific mouse source, in case the data was gathered from multiple mice/donors. …

In that case, I really think you should leave in the "structure(" "structure_sets_structures(" "structure_set[name$eq'Developing Mouse - Coarse']" ")" ")," from my example code. The way you have edited the API call, the qu…

And to be clear, now that I think a bit more about your output, this FOUND 2106 GENES IN 1.81e+02 SECONDS ====START GETTING ACTUAL EXPRESSION DATA==== QUERYING GENE IDs 11134 through 14582 EXPECT TO FIND 3277514 DATA ENTRIES means that there were 3.3 million rows associated with the first 500…

Batch download: Developing mouse brain

Technical

danielsf August 7, 2025, 4:11pm 6

I would like to take a step back and ask what you want this data to look like? If you do not want the structure unionization data, do you want something like the data described in this section of the documentation (gene expression quantified over a 3D grid of the brain)?

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Batch download: Developing mouse brain

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