Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Accessing multiresolution neuroglancer data #4

Open
tathey1 opened this issue Jan 28, 2025 · 1 comment
Open

Accessing multiresolution neuroglancer data #4

tathey1 opened this issue Jan 28, 2025 · 1 comment

Comments

@tathey1
Copy link

tathey1 commented Jan 28, 2025

I often use CloudVolume to access precomputed data that is stored on some server. Is it possible to use this to access the ome-zarrs that are being served for BIL neuroglancer visualization?

I'm asking because, while standard BIL downloads (e.g. here) only offer a couple sampling resolutions (e.g. 0.35x0.35x1, 0.35x0.35x100, 3.5x3.5x100), it seems like the ome-zarr copy of the data has more resolutions available.
My goal is to be able to, in python, select a resolution level, then download a specific spatial area (e.g. using numpy-like indexing). Do you have any example code snippets that do something like this?

@AlanMWatson
Copy link
Member

Hi Tom,

If you search for a dataset at BIL and it returns a visualization link, then we have a converted version of that data that can be accessed through BrAinPI.

Serarch results for mouseID_405426-182724:
https://api.brainimagelibrary.org/web/list?fields=FullText&searchtxt=mouseID_405426-182724

The dataset landing page:
https://api.brainimagelibrary.org/web/view?bildid=ace-bag-kit

The visualization link:
https://brainapi.brainimagelibrary.org/ng/bil/assets/ace/bag/kit/asset/brainpi/mouseID_405426-182724.omehans

This is also the link to the the precomputed version of the data. just add /info to get the metadata file:
https://brainapi.brainimagelibrary.org/ng/bil/assets/ace/bag/kit/asset/brainpi/mouseID_405426-182724.omehans/info

The path_to_html_options endpoint returns several file format options. There is no easy way yet to get to this endpoint yet, but if strip the /bil/assets/... portion of the neuroglancer link and pass it to the endpoint as below it will return links to several dataformats including ome-zarr:
https://brainapi.brainimagelibrary.org/path_to_html_options/?path=/bil/assets/ace/bag/kit/asset/brainpi/mouseID_405426-182724.omehans

Let me know if you have any other questions.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants