Downloading comprehensive list of SectionDataSets for ISH data

Technical
1

Hi all – I’m trying to download a complete list of the coronal SectionDataSets for the Adult Mouse Brain, as well as the Developing Mouse Brains separately. Ultimately, I’m trying to download the density expression data from the ISH experiments for every single gene, so I can run various analyses for my lab. Is there an easy way to do this?

I can do gene searches but it’s a very slow way to get it. There should be 20,000 SectionDataSets, if not more for the Adult Mouse Brain data, given there are 20,000 genes covered. The API and SDK aren’t clear on how to do this (I’ve tried many different ways).

Thanks for any help.

2

Hi @robcahill10

Can I confirm what it is you want to download?
Did you want the density expression for each structure for each image-series?
Or are you after the voxel level data?

3

I’m looking for the voxel level data. For example, here is a link to download the voxel-level data (67x41.58) for the SectionDataSet 73521808, from the coronal view, for the gene Stard8: http://api.brain-map.org/grid_data/download/73521808?include=density.

I’d like to get the full list of SectionDataSets (like 73521808, plus all the other 1000s of SectionDataSets), so I can combine them all into a single data set, one for adult mouse brain, and then later, one for each stage of developing mouse brain. Then, that will allow us to analyze patterns in gene expression.

4

You can use the API to get such a list using the query below.
20k+ record is too much to fetch at time.
I would recommend getting around 1000 record at a time and increment the “start_row” parameter.

http://api.brain-map.org/api/v2/data/query.xml?criteria=
model::SectionDataSet
,
rma::criteria,
[failed$eqfalse],products[id$eq1],treatments[name$eqISH]
,rma::options
[start_row$eq0]
[num_rows$eq1000]

The “Mouse Brain” Atlas is product = 1
The “Developing Mouse Brain” Atlas is product = 3

5

This works! Thank you!

6

Two more questions:

  1. For the query referenced in the comments above, how do I specify the stage (e.g. p56 vs. p4)?

  2. I’m trying to pull the related atlases to match brain area with gene expression. For example, for the adult mouse brain, I have the CCF adult mouse brain atlas (that our lab isn’t sure how we got originally) in two files: one is 12x66x40x57 (which connects the ISH density data to areas in the brain) and one is 12x18 for the higher level structures. How can I pull those files for each stage of the developing mouse brain?

Appreciate the help.