bioformat fails to read tiff files from Carl Zeiss Nvision40

[lawa]

Hi

the bioformats plugin fails to read tiff files created by Carl NVision tools. It works fine using the default image reader for tiff but the bioformats filter fails. This is annoying as it prevents a successful import into omero.

If the images are read by bioformats I get metatdata but a black image only. If I use the normal imagej open I get the image but no metadata

There is a related issue with no solution in the omero forum dealing with pictures from a Zeiss Supra

viewtopic.php?f=4&t=7934&p=16511&hilit=zeiss#p16417

Gregor

[dgault]

Hi Gregor,

Thank you for following up on this issue, I will try and further investigate a fix to the problem and see if a solution can be put in place.

In the mean time if you have any sample files which could be used to help test this issue they can be uploaded to the following link: https://www.openmicroscopy.org/qa2/qa/upload/

With Thanks,
David Gault

[dgault]

Hi Gregor,

Just as a follow up to my investigation, the original issue you mentioned with the displaying of blank pixels has had a fix applied in one of the more recent versions of Bio-Formats. If you update your Bio-Formats jar to the latest revision this should hopefully resolve the problem.

In Fiji you can update the plugin through Plugins -> Bio-Formats -> Update Bio-Formats Plugins

With Thanks,
David Gault