[ome-users] Position of scenes in CZI files

[Balaji Ramalingam (Staff)]

Hi,

Thank you for sharing your issue.

Please take a look at the following code-blocks from the Bio-Formats CZI reader,

The stage positions are being read under certain conditions,
https://github.com/openmicroscopy/bioformats/blob/develop/components/formats-gpl/src/loci/formats/in/ZeissCZIReader.java#L1228
https://github.com/openmicroscopy/bioformats/blob/develop/components/formats-gpl/src/loci/formats/in/ZeissCZIReader.java#L1240
https://github.com/openmicroscopy/bioformats/blob/develop/components/formats-gpl/src/loci/formats/in/ZeissCZIReader.java#L1252

And
The series/scene information is being read under certain conditions as well,
https://github.com/openmicroscopy/bioformats/blob/develop/components/formats-gpl/src/loci/formats/in/ZeissCZIReader.java#L1153

Could you please submit a sample file to the following link,
https://www.openmicroscopy.org/qa2/qa/upload/

This would help us troubleshoot your issue in better detail.
Thank you,

Best,
Balaji


On 20/07/2017, 15:32, "ome-users on behalf of Nick Trahearn" <ome-users-bounces at lists.openmicroscopy.org.uk on behalf of nick.trahearn at icr.ac.uk> wrote:

    Dear All,

    Recently I've been working with CZI images using BioFormats. I'm not overly familiar with the format and its various forms but, in the images I have, each detected tissue section is placed into its own separate series (or scene, as they are called in Zeiss' viewer). I want to be able to stitch series together, relative to their original positions on the slide, in order to turn these individual sections back into a continuous image. Most of the tools required to do this are already available within BioFormats' ZeissCZIReader, but, as far as I can tell, there isn't a way to get the relative position of a series. It would be reasonably easy to add this into the existing reader, requiring just a few small additions, but I wanted to ensure that I hadn't missed anything obvious before I opened a pull request.

    All the best.
    Nicholas Trahearn.

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