Programmatic download of human ISH - issues with allensdk

Technical
,
1

Hello @SvenOtto @racheld @tylermo

I am planning a study that uses a large amount of ISH data from the human database and was wondering how I could retrieve that data programmatically (autism study). I know there’s a python notebook but the allensdk doesn’t seem to work on my computer (MacBook Pro M3Pro Apple Silicon Chip running MacOS Sonoma). I tried

pip install allensdk
and I get the following error message :

image
image897×841 149 KB

Here is the link to the jupyter notebook I am trying to run : image_download

I am trying to run my jupyter notebook through anaconda navigator + jupyter version 7.4.4. The version of python is python 3 (ipykernel)

Because I know I can retrieve section dataset images, if I provide the ID number for an ISH experiment like the one for NEFL I should be able to retrieve those.

Not sure why it’s not working, but any help would be greatly appreciated. Thanks!

2

Hello,

Thanks for using the AllenSDK. We believe this is related to a known issue in which installing “numpy<1.24” causes this failure. As a workaround I’d recommend creating a virtual environment for an older version of python, installing the AllenSDK without dependencies and then manually installing the dependencies. We’ve had other users report success using this method.

There’s work in progress to address this which you can see here: https://github.com/AllenInstitute/AllenSDK/pull/2768

Apologies for this inconvenience - hopefully this helps you get started in the meantime!

Thanks,

Ray

1 Like
3

Thank you so much @ray.sanchez since making the virtual environment, I’ve been able to get around the issue!

(I’ve also been successful without the virtual environment on a M1 Ultra MacStudio running MacOS Ventura).

I did have another question though. I am using the image download notebook to retrieve ISH images. I know by providing the experiment ID number (for the section dataset) I can retrieve the set of colorimetric ISH images, but is there a way to retrieve the Expression images from the python notebook? So far I’m only able to download them manually from the database itself. If there’s a way, please let me know.

Thanks,

MP