[ome-users] BioFormats Update

[David Gault (Staff)]

Hi Skye,

This is not something that we were aware of as an issue so thank you for bringing it to our attention. I retested the fix from 5.4.0 but did not see any regression with the sample files that we currently have.
If you are able to provide a file that shows this issue then we can further debug the problem. Any sample files can be submitted via the link below:
https://www.openmicroscopy.org/qa2/qa/upload/

With Thanks,
David Gault

On 12 Jul 2017, at 17:56, Skye McBride <smcbride at uottawa.ca<mailto:smcbride at uottawa.ca>> wrote:


I am writing from the Cell Biology and Image Acquisition Core facility at the University of Ottawa. I recently noticed that we are having issues again with the BioFormats importer from colour images in the .zvi format. Previously this issue was resolved for our 12-bit colour images with the release of 5.4.0 (see below) and I had identified that it was the RGB channel count that was causing our images to open not as RGB but rather as a GGB image. Do you know if this is something that is being worked on?

BioFormats 5.4.0
*   Zeiss AxioVision ZVI (Zeiss Vision Image)
     *   ensure that the bitsPerPixel field is always set to match the final pixel type, and populate any channel colors that were parsed in the metadata. The bits per pixel update should only affect uint16 or int16 files where the acquisition bit depth is not a multiple of 8, and the RGB channel count is greater than 1


Thanks in advance for any insight/help you can provide,


Skye McBride, MSc
Microscopy and Imaging specialist
Cell Biology and Image Acquisition Core Facility
Faculty of Medicine
University of Ottawa
Room 3171
451 Smyth Road
Ottawa, ON K1H 8M5
Office: 613-562-5800 ext: 8983<tel:613-562-5800%20ext%3A%208376>
CBIA core facility <http://www.med.uottawa.ca/research/corelabs/CoreLabs_CBIA/eng/>



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