Examples for Microscopy BEP031

[mariehbourget]

This PR provides 2 example datasets for Microscopy data (BEP031, @mariehbourget, @jcohenadad).

• micr_SEM: 1 sample, multisession, in PNG format
• micr_SPIM: 2 samples, with multiple chunks, in OME-TIFF format

As discussed, OME-TIFF files are small 1x1x1 pixel files in order to preserve metadata for validation.

The microscopy validator is not ready yet but should follow in about 2 weeks.
The example datasets may be updated while finalizing the validator and after community review of the BEP031 spec.

Thanks to @etiennebergeron for his help building the datasets!

[Remi-Gau]

Small thing to add when this is ready to merge (not urgent)

a summary table in the README.md of the repo

https://github.com/bids-standard/bids-examples#dataset-index

[guiomar]

Hi @mariehbourget! I think that it might be convenient that the 4 chunks of the samples A and B of the example microscopy/SPIM001 have a corresponding json file, indicating the ChunkTransformationMatrix.
I think (in line with what we had discussed for the specs), this may help to ilustrate the use of this new chunk feature.

[mariehbourget]

Hi @mariehbourget! I think that it might be convenient that the 4 chunks of the samples A and B of the example microscopy/SPIM001 have a corresponding json file, indicating the ChunkTransformationMatrix. I think (in line with what we had discussed for the specs), this may help to ilustrate the use of this new chunk feature.

Hi @guiomar, thank you for this suggestion. I had a similar thought yesterday. My issue is that those examples are "empty" data. So they are just empty 1x1x1 pixel files. I was wondering if adding chunk transformation to empty images would be more confusing. But I agree this could help to have an example so I think we could explain it in the README of the dataset.
I'll keep you updated with the progress on this.

[mariehbourget]

Hi @Remi-Gau, we are updating our examples and have a small question.
For the microscopy examples in this repo (and the external examples we put together), what should be the BIDSVersion in the dataset_description.json file?
It is 1.6.0 at the moment but that version does not include microscopy. Should we put v1.6.1-dev (current version of the "latest" doc) or 1.7.0 (even though 1.7.0 is not released yet)?
Thanks!

[Remi-Gau]

Hi @Remi-Gau, we are updating our examples and have a small question. For the microscopy examples in this repo (and the external examples we put together), what should be the BIDSVersion in the dataset_description.json file? It is 1.6.0 at the moment but that version does not include microscopy. Should we put v1.6.1-dev (current version of the "latest" doc) or 1.7.0 (even though 1.7.0 is not released yet)?

I would say that it should be 1.7.0. One of the long term goal would be to have the validator check that a dataset fits the requirements of the BIDS version mentioned in the description. For you it will be version 1.7.

That being said I just realized that this means that some of the BIDS datasets for PET need to have their version number bumped up to 1.6.0. @mariehbourget are you sure you don't want to join us as maintainers: you definitely have a knack for internal consistency. 😍 👍

[mariehbourget]

Following the Microscopy BEP community review, we will update the examples in this repo in-parallel with the implementation of the validator.
Here is a list of the changes that will be made:

• In SPIM: Add 1 JSON file per chunk with examples of the ChunkTransformationMatrix and ChunkTransformationAxis field, with explanation in the README.
• Update the value of the SampleEnvironement field to "ex vivo" instead of "exvivo", both in SEM and SPIM.
• Update data type to micr instead of microscopy, both in SEM and SPIM
• Update BIDSVersion to 1.7.0 in dataset_description.json of both SEM and SPIM
• Add a summary table in the README.md of the repo
• Corrections to OME-TIFF XML metadata

[mariehbourget]

@guiomar, as you suggested, we added examples of the ChunkTransfomrationMatrix and ChunkTransfomrationMatrixAxis fields in the JSON files of the micr_SPIM example dataset.

@Remi-Gau, the examples are completed with the latest changes from the community review. I also included the summary table in the README.md file.
EDIT: we found some issues in our OME-TIFF XML metadata, we will need to update the files soon (so not completed yet)

[mariehbourget]

Just as a follow-up:
The OME-TIFF XML metadata are corrected.
The examples are now complete.