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Adding micr_XPCTzarr dataset #455

Merged
merged 20 commits into from
Aug 27, 2024
Merged

Adding micr_XPCTzarr dataset #455

merged 20 commits into from
Aug 27, 2024

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chourroutm
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Addition of an example dataset for the XPCT suffix for microscopy in the OME-Zarr (NGFF) file format.

@chourroutm chourroutm marked this pull request as draft July 12, 2024 15:46
@chourroutm chourroutm marked this pull request as ready for review July 26, 2024 15:18
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@effigies effigies left a comment

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Rebased to simplify merging. Apologies, I didn't realize this was your main branch.

Two small suggestions you can merge directly through github.

micr_XPCTzarr/participants.json Outdated Show resolved Hide resolved
chourroutm and others added 2 commits August 6, 2024 19:45
Co-authored-by: Chris Markiewicz <effigies@gmail.com>
…oto.json

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
@effigies
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effigies commented Aug 6, 2024

@bids-standard/maintainers This PR uses a BIDS-URI. These are supported by the schema validator but not the legacy validator. Do we just want to exclude this dataset from legacy validation, or fall back to the subject-relative path?

@sappelhoff
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Do we just want to exclude this dataset from legacy validation

+1 to exclude from legacy validation

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effigies commented Aug 7, 2024

Did https://github.com/bids-standard/bids-validator/pull/2069 instead. Running locally, only EMPTY_FILES complains:

bids-validator/bin/bids-validator ../examples/micr_XPCTzarr
bids-validator@1.14.9-dev.0
	1: [ERR] Empty files not allowed. (code: 99 - EMPTY_FILE)
		./sub-01/ses-01/micr/sub-01_ses-01_sample-brain_XPCT.ome.zarr/0/0/0/0

	Please visit https://neurostars.org/search?q=EMPTY_FILE for existing conversations about this issue.

	1: [WARN] Tabular file contains custom columns not described in a data dictionary (code: 82 - CUSTOM_COLUMN_WITHOUT_DESCRIPTION)
		./samples.tsv
			Evidence: Columns: sample_info  not defined, please define in: /samples.json

	Please visit https://neurostars.org/search?q=CUSTOM_COLUMN_WITHOUT_DESCRIPTION for existing conversations about this issue.

        Summary:                  Available Tasks:        Available Modalities: 
        12 Files, 136.75KB                                Microscopy            
        1 - Subject                                                             
        1 - Session                                                             


	If you have any questions, please post on https://neurostars.org/tags/bids.

@effigies effigies merged commit d90c132 into bids-standard:master Aug 27, 2024
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5 participants