Question regarding location of datasets

[anwai98]

Hi @JoOkuma,

First of all, thanks for your work!

Have you released the data used in your preprint (besides the one from CTC) (and the corresponding segmentations)? If yes, can you hint me on how to access it? (I am sorry if I missed the mention in the documentation)

[JoOkuma]

Hey @anwai98, thanks for the kind words.

The publicly available data is available here, I included a brief readme describing the files.

I'm waiting for a colleague for the neuromast annotated tracks; I'll give you an update when that's done.

We haven't completely curated the datasets' segmentation masks and we were mainly evaluating at the track level, so only those are available.

We are only making the densely labeled channel available for the multi-channel zebrafish embryo because we might create a benchmark in the future and want to avoid data leakage with the test set. If that's not materialized soon, we will make it publicly available.

Let me know if you have any trouble accessing the data.

[anwai98]

Hi @JoOkuma, thanks for the response!

The publicly available data is available here, I included a brief readme describing the files.

Ahha nice, thanks. I'll check it out.

And thanks for sharing all the information. I'd be happy to check out the updated datasets coming in as well (once they are out).

Btw, can you suggest a way to download the files stored at https://public.czbiohub.org/royerlab/ultrack using python scripts? (I can only seem to click over the tif files for download, the rest (eg. zarr files) just allow me to access items over the container, not a central download) (unless I am missing something)

[JoOkuma]

@anwai98, I mainly used wget from the terminal

This should work as well:

import urllib.request
urllib.request.urlretrieve("https://public.czbiohub.org/royerlab/ultrack/multi-color-cytoplasm.tif", "multi-color-cytoplasm.tif")

StackOverflow reference

For Zarr, you could use their copy function to move from a remote to local storage.