[ome-users] ScanR file conversion to OME Tiff - feature request

[Volker Hilsenstein]

Dear OME users/developers,

I have a feature request regarding the handling of ScanR data, in
particular when doing a batch conversion to OME tiff.
First off, I have to admit that I'm only superficially familiar with
bioformats/LOCI but I have inherited some legacy code
from a software engineer that now works elsewhere.

First off, a short problem description: we are a microscopy facility and we
use the ScanR microscopes for many of the high-throughput screens
run by our users and visitors. We use a legacy script that calls bioformats
for converting the ScanR tiff files to OME tiff with an OME tiff filename
convention. For this script the software engineer forked an earlier version
of bioformats and made some modifications.

>From my understanding the main modification added by our software engineer
was to address the following issue:

Apparently, the ScanR output contains a list of all the filenames of the
run as Metadata. For a large well plate with many subpositions this can be
several thousands of file names, which are often very long due to deeply
nested paths. When running a batch conversion this Metadata gets added to
the header of each individual tiff image, which can increase the size of
each image by several megabytes.

He also added some other changes, but I am fairly confident these could be
added outside of the main bioformats code.

>From our point of view, it would be convenient if the possibility of
stripping the list of filenames from the metadata was added as an option to
the main branch of bioformats. Is this something you'd be willing to
consider?

Kind regards,

Volker
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