Open FLIM File Format

Data Management
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#1

Browsing the OME website in search of an open file format for FLIM data which I could use for my own application, I ended up on this page:

which lists a gazillion formats (which it would be nice to be able to sort according to the different categories…), the “greenest” one being, of course, the OME ones (OME-TIFF and OME-XML).
Notwithstanding the absence of a working link to OME-TIFF specification docs on that page (but the actual specs can be found here: The OME-TIFF format — OME Data Model and File Formats 6.2.0 documentation), I am wondering whether the community could chip in on their favorite FLIM file format (open, not linked to a specific vendor, as I am using custom instruments).

The OME-XML specification page seems to have been last updated in 2016… but the reason is explained in an unrelated page: The OME-XML format — OME Data Model and File Formats 6.2.0 documentation, so OME-TIFF seems to be the way to go. However, I am unclear how FLOAT images would be stored in such a format (e.g. phase and modulus data for a phasor image),

#2

Hi @smXplorer,
I don’t work with FLIM data myself but I know that Ian Munro at Imperial College has done a lot of work in that area and they produced the FLIMfit package which interacts with OMERO. See: https://flimfit.org
Maybe there’s something in there for what you need?

Also, there is a large effort to develop a next generation container for storing image files under the tag #ome-ngff in this forum. It would be useful to provide your input to that effort to make sure such a future storage format/container is appropriate to store FLIM data.
Cheers,
Damir

#3

Thanks for the pointers.

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#4

Also see the Modulo annotation which can be used to split the “C” dimension into subdimensions, so you can add separate “phase” and “modulus” channels this way. At the Image/Pixels level you set SizeC=2 and then split the two into 1xphase and 1xmodulus with the annotation.

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#5

OK, thanks. I’ll start from here.