Not able to download or view Human ISH data

How To Allen Human Brain Atlas
1

Hello,

I’ve been trying to access the Allen Human Brain Atlas ISH Database, and I have notived that I’m not able to view or download any image data from the website. I’m interacting with the cortex study, and this has been persisting for ~48 hours now.

I have tried using chrome and safari - working on a Mac myself, and I am still encountering this problem. Are others experiencing issues at this time or is it just me?

Please let me know.

Thanks!

2

Hi @MPanday,
Thank you for bringing this issue to our attention. It should now be resolved.

Please let us know if you continue to run into any issues.

3

Thanks @SvenOtto I’m now running into another issue, this time with the BrainSpan Atlas. I am trying to download the Nissl images from the adult human reference atlas at image quality 100 (full) with now downsampling (full resolution) and on my Mac I’m getting an error message that the image cannot be opened once it’s downloaded. Do you have any ideas as to what could be causing that?

Please let me know.

Thanks.

4

Hi @MPanday ,
Could you provide more details on the issues you’re experiencing so we can assist you better:

  1. Is this true for all images or just some?

  2. Example image IDs that you’re experiencing the issue with?

  3. Mac OS version and software you’re trying to open the images with?

Thank you for your patience.

5

Hi @SvenOtto to respond to your questions:

  1. this is true for Nissl-stained images of whole coronal sections from the brainspan reference atlas (postnatal brain 34 years female, and the prenatal cerebrum reference atlas as well)

  2. I’m experiencing the issue with all the Nissl images. I’ve included a screenshot here of the settings I have set for the image I’m trying to download. I tried downloading the current view and I don’t have any issues, it’s only when I try downloading the “Entire Image”

    image
    image800×662 110 KB

  3. I am on a MacBook Pro with an M3 Pro chip (Apple Silicon), and running MacOS Sonoma. I’m trying to open the images in Preview and I get the following error message when I try opening the images. I’ve attached here a screenshot of the message here:

    image
    image520×528 41.7 KB

Please let me know if there is anything else you need as you look into this. I really appreciate it!

Thanks and best,

MP

6

@MPanday, thank you for your patience.

We tested this internally and were all able to reproduce the issue for those particular images. We’ll investigate and get back to you soon.

7

Thank you very much @SvenOtto, I appreciate it!

8

@MPanday , thank you for your patience.

Unfortunately, we’ve discovered that fixing the images download in the app won’t be possible any time soon.

We could consider making the data available in an S3 bucket w/ a python library to use their proprietary format in the future.

Is that something that would be useful to you?

9

Hi @SvenOtto thanks for letting me know. Yes, that would be very useful as I am currently planning a study that would require the reference atlas Nissl images.

Additionally, I do have a question about the ISH database. Is there a Jupyter notebook or other accessible computational pipeline for processing ISH images to make the expression images? As of right now, I can only download them from the database, but if I wanted to process my own anatomy images in the same way, is there a workflow for that that I can follow? Please let me know.

Thanks again!

MP

10

Thank you for the feedback.

I’ll document this ask for future consideration. I can’t give a timeline estimate at this time beyond “likely in 2026” but we’ll circle back here when the images are available through new channels.

Thank you for your interest and patience.

11

Thank you so much @SvenOtto for letting me know and for looking into this issue. I would like to circle back onto my earlier point about expression images though. Is there a documented pipeline or computational workflow end users can access?