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

[Melissa Linkert]

Hi Volker,

> 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?

We would certainly be happy to consider bringing these changes back
into the official repository.  Probably the best thing is if you can
send a copy of changes that were made, either as a diff or as a GitHub
pull request against Bio-Formats' repository:

http://github.com/openmicroscopy/bioformats

We can then review and determine if any modifications need to be made in order
to get those changes merged into the main branch.

Regards,
-Melissa

On Thu, Feb 28, 2013 at 02:45:25PM +0100, Volker Hilsenstein wrote:
> 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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