[ome-devel] bfconvert 5 produces 16-bit tiff files that cannot be read by freeimage

[Roger Leigh]

On 08/08/2016 10:45, Tjelvar Olsson (JIC) wrote:
> Dear Roger,
>
> Thank you for your explanation. It makes sense.
>
> However, I think it would be useful if it was possible to convert the images with the colour map stripped out, i.e. replicating the previous behaviour of bfconvert. This enables the creation of TIFF files that can be more easily understood by computers. In this case the colour map does not contain "information", it is rather a means to aid the human looking at the image. From the computer's point of view this information is stored in the channel index.
>
> Would it be possible to add a flag to the bfconvert tool not to transcribe the color map?

Yes, I think so.  Please see

https://trac.openmicroscopy.org/ome/ticket/13273
https://github.com/openmicroscopy/bioformats/pull/2515

I hope this will meet your needs and create suitable TIFF images using
min-is-black photometric interpretation.  It's certainly behaving as
expected for me with some sample Zeiss LSM images.

This patch is for Bio-Formats 5.2, but it will also apply to 5.1.


Regards,
Roger

--
Dr Roger Leigh -- Open Microscopy Environment
Wellcome Trust Centre for Gene Regulation and Expression,
School of Life Sciences, University of Dundee, Dow Street,
Dundee DD1 5EH Scotland UK   Tel: (01382) 386364

The University of Dundee is a registered Scottish Charity, No: SC015096