OME Bdv file format

#1

Hi @s.besson @dgault @joshmoore,

Do you already have specifications of the ome-bdv format?

Specifically, we are wondering whether it would also support

  1. diverse image loaders: <ImageLoader format="XYZ">, or would it only support hdf5?
  2. affine transformations: <affine>1000.0 0.0 0.0 0.0 0.0 1000.0 0.0 0.0 0.0 0.0 1000.0 0.0</affine>

?

Cheers,
Christian & @schorb

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#2

Hey @Christian_Tischer et al.

The simple answer is, unfortunately, no. There are a number of things this encompasses, including in roughly the order you might expect them to appear:

  1. A link between the BDV-XML model and the OME-XML model
  2. An extension/replacement for the <TiffData/> element to point to BDV-HDF5 data
  3. Application of the new element to point to new data containers like Zarr/N5 v3.

One preliminary that is potentially also worth some investigation is storing a companion OME-XML file alongside an existing BDV dataset such that there’s an implicit link between the two.

In general, an open OME-* file format can’t be expected to understand all the proprietary file formats understood by Bio-Formats. But loading at least more than one file format will leave the door open for future support.

Capturing the spatial context of the images is certainly going to be required, yes. Additionally, there will likely need to be a new generic field-of-view model in OME that lies between the simple bag-of-images concept (OME’s “Datasets”) and the highly modeled Plates.

~Josh

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