Configurable splitting into multiple files

[tischi]

Hi,

In the Fiji Bio-Format plugin one can choose (multiple-choice):

• Split channels into separate files
• Split time points into separate files
• Split z planes into separate files

It would be very useful to have such functionality also in raw2ometiff and eventually also in the ngff-converter (see https://forum.image.sc/t/ngff-converter-2-0-released-convert-bioformats-to-ome-ngff-ome-tiff/96102/16).

Example use case: 3-D movie that one wants to process with CellPose, which only takes individual 3-D volumes.

[sbesson]

Thanks for opening this issue,

See #80 and #108 for the previous efforts to extend the converter and support additional OME-TIFF layouts. Reflecting on this work, the primary challenges were:

• the expectation in terms of format/layout. In the example above, is the aim to support all combinations of options? What about multi-series/multi-images? Are there expectations in terms of file naming?
• the extra complexity in the implementation especially if the number of supported layouts grows
• the amount of testing required to validate the new layouts as well as the supported layouts against a wide range of imaging modalities

We appreciate both this request and the previous layout improvements were driven by the requirements of third-party analytical tools (CellProfiler, CellPose) in terms of data input. As addressing such issues can be done either from the writing side or the reading side, have you raised with the maintainers of the library whether the existing OME-TIFF filesets could be used and what was their response?

Based on my reading, it looks like CellPose also supports Zarr as an input. Would an alternative workflow would be to convert the original data into OME-Zarr using bioformats2raw and then point CellPose at the relevant multiscales group or Zarr array?