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?
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!