bids-standard/bids-examples

access microscopy example data

Closed this issue · 8 comments

tischi commented

hi, thanks for this great effort!

there are no links here for download: https://github.com/bids-standard/bids-examples#microscopy-datasets

is that data available somewhere?

Remi-Gau commented

I think @tischi meant the dataset where those examples were extracted from.

for example see the column link to link to full data in the table here:
https://github.com/bids-standard/bids-examples#mri-datasets

Screenshot from 2023-05-08 12-31-12

hermancollin commented

You are right. I don't know about micr_SEMzarr and micr_SPIM. I'll ask around for the latter, which was uploaded by our group. In the meantime, the full data for micr_SEM is hosted on github here: https://github.com/axondeepseg/data_axondeepseg_sem.

I'll open a PR to add the links.

hermancollin commented

hmm actually I do not have writing access to this repo so I can't open a PR myself. However, I found the missing links for these two:

mariehbourget commented

hmm actually I do not have writing access to this repo so I can't open a PR myself. However, I found the missing links for these two:

Hello everyone!

The micr_SEM and micr_SPIM datasets on bids_examples (https://github.com/bids-standard/bids-examples/tree/master#microscopy-datasets) are "dummy" datasets created only for testing the folder hierarchy, file naming and metadata with the BIDS-validator. So there are no link to the full data for those.

The links to zenodo are real data examples datasets (compliant with BIDS but not related to the bids_examples):
SEM real data example: https://doi.org/10.5281/zenodo.5498378
SPIM real data example: https://doi.org/10.5281/zenodo.5517223

Remi-Gau commented

probably worth adding some of that info in the README of the bids example repo

jcohenadad commented

probably worth adding some of that info in the README of the bids example repo

@hermancollin would you mind doing this? thx!

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