example microscopy data in the zarr format is missing a sidecar

[robertoostenveld]

@effigies pointed me to this zarr example in this comment.

The specific subject and session comprises a SPIM (zarr) and a SEM (png) image. The zarr file has no sidecar JSON, although the spec states that to be required.

[effigies]

Cc @TheChymera, who I think prepared this example.

[TheChymera]

@robertoostenveld but it has a JSON file:

[deco]~/src/bids-examples/micr_SEMzarr/sub-01 ❱ ls */micr
ses-01/micr:
sub-01_ses-01_sample-A_SEM.json  sub-01_ses-01_sample-A_SEM.png  sub-01_ses-01_sample-A_SPIM.ome.zarr

ses-02/micr:
sub-01_ses-02_sample-A_SEM.json  sub-01_ses-02_sample-A_SEM.png
[deco]~/src/bids-examples/micr_SEMzarr/sub-01 ❱ cat ses-01/micr/sub-01_ses-01_sample-A_SEM.json
{
        "Manufacturer": "Hamamatsu",
        "ManufacturersModelName": "C4742-95-12G04",
        "BodyPart": "CSPINE",
        "SampleEnvironment": "ex vivo",
        "SampleFixation": "4% paraformaldehyde, 2% glutaraldehyde",
        "SliceThickness": 1,
        "TissueDeformationScaling": 98,
        "PixelSize": [0.18, 0.18],
        "PixelSizeUnits": "um"
}

[effigies]

That's the png file that has a sidecar, not the microscopy file. The suffixes need to match.

[TheChymera]

ah, ok.

[TheChymera]

@effigies @robertoostenveld does this solve the issue?

#386

[robertoostenveld]

Yes. It is a very minimalistic sidecar, but as far as I can tell, it fulfills the requirements.

thanks!