[Brainspan ISH] Atlas Image to Section Image

Technical
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1

Hi,

I would like to retrieve the list of section_images corresponding to a list of reference images for a specific atlas, but I can’t figure out how to do this.

For example, for atlas_id 138322603 , the pcw 15 developing human atlas, I have selected 4 sections that best represent the areas I am interested in.
In my drawing, these would be images 1:4.

Their section image ids are:

102125611
102125569
102125613
102125599

For a given section dataset, eg. 100135098 (an ISH experiment for SATB2 in 15 pcw) how can I get the sections closest to each of the 4 atlas images?

I tried using the image_to_image function but get an empty response.

section_datasets = requests.get("http://api.brain-map.org/api/v2/image_to_image/102125613.json?x=1&y=1&section_data_set_ids=[100134510]).json()"

There is an image_to_atlas function in the AllenSDK but I need the reverse.

I also tried getting the transform values for the section images as suggested in Matching experiment section images with brain segmentation, but no success there either.

# Example API query to get transform values at the SectionImage level:

"http://api.brain-map.org/api/v2/data/query.json?criteria=model::SectionImage,rma::criteria,[data_set_id$eq524874308[section_number$eq14],alignment2d,rma::include,alignment2d"

Any help is much appreciated.

image
image2330×2420 455 KB

Thanks! :slightly_smiling_face:

2

Hi @carmen.se,

Unfortunately, the image_to_image, and image_to_atlas functionality is mainly restricted to whole mouse brain image data where we have developed a 3D reference and a mapping pipeline. As such, there isn’t information in the database to directly make the query that you want.