Programmatically accessing Human ISH

Hi there,

I’m working with the Allen Human Brain ISH database, and I’m trying to retrieve large amounts of image data for a neuroanatomy project involving cell morphologies.

I know from my previous work with the mouse brain ISH that there is a jupyter notebook linked here that works to retrieve and organize images along with their metadata.

I have not been able to do this with the human ISH database. Every time I supply human experiment IDs, the code throws several errors, and cannot connect or find the datasets in question.

Is there a way to programmatically access human ISH data without downloading single images manually from the database?

Please let me know.

Thanks!

Hi Maheshwar,

Can you share some of the errors you’re getting?

Tyler

Hi @tylermo

I’m currently working on a project with the human brain ISH data from the visual cortex in the cortex study. I have been having troubles downloading the images and I came across this post which seems to the same error I am having.

I have tried modifying the Python code provided in the Downloading Images file: image_download

I haven’t been able to successfully download the images because the dataset ID is not available for the samples that I’m working with. I tried to replace the dataset ID with the specimen ID, but this isn’t returning anything because the section_image_query() function requires a dataset ID. Using the specimen links (like this one, for example: Specimen Detail :: Allen Brain Atlas: Human Brain), I downloaded the specimen-specific XML files and tried to find a dataset ID but it doesn’t exist, so this method of downloading doesn’t work for these examples.

Any help or guidance would be greatly appreciated, thanks!