BIDS with histology data

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This looks like a great start! I like the list of modalities, which looks consistent with how BIDS approaches it.

From a quick look, here are some thoughts:

  • You’ll probably also want to consider any metadata relevant to the interpretation of an image. For instance, perhaps certain microscope vendors, models or settings would be worth recording.

  • For histology, stains and dyes might be worth promoting into the filename to help distinguish things. In MRI, we have ceagent (contrast-enhancing agent), which might be close enough semantically to be reused here, for example, sub-01_ceagent-nissl_OM.tiff.

  • I’m not really up on my histology, so this may be a dumb suggestion, but if there’s only one way to image a given stain or dye, it’s possible that it would make more sense to promote these to the level of modality, instead of SEM/TEM/OM/CARS.

  • Organ or structure might be worth promoting into the filename as well.

  • In any event, I would strongly suggest settling on a single file format. The advantage of BIDS is that by constraining what data is BIDS, the more downstream tools can depend on it and spend more code on processing and less on handling disparate inputs. I would advocate a lossless format. For the sake of random-access, image compression algorithms may not be ideal. TIFF would probably be my suggestion.

  • You can also consider something like NIfTI, which permits 2-dimensional images and includes an affine matrix that can be used to provide information like the pixel size, direction of each dimension in anatomical coordinates. This would obviate your PixelSize and Fov metadata, and NIfTI can encode RGB values as well as scalars. The obvious downside is that histological tooling may not support NIfTI.

I agree with Franklin that this would be a good discussion to open on the GitHub issues to get further guidance on integrating with BIDS. It would also be good to try to reach out to other labs doing histology or labs/companies working on analytical software. Broad input (and commitment to implement) is critical for designing a standard that people use.

cc @crocodoyle

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