[ome-users] open Carl Zeiss 2011 .czi files of transmitted light images correctly

[David Gault (Staff)]

Hi Pierre,

Thanks for reporting this issue, there have been a number of bug fixes to the CZIReader in recent releases which may have resulted in this.
In order for us to debug this problem would you be able to upload a sample file that shows this problem to the link below:
https://www.openmicroscopy.org/qa2/qa/upload/

With Thanks,
David Gault

> On 29 May 2017, at 17:33, Godement Pierre <pierre.godement at ens-lyon.fr> wrote:
>
> Hello
>
> seems that the latest version of FIJI and/or the Bioformats package cannot open Carl Zeiss 2011 .czi files of transmitted light images correctly unless these are made with the latest ZEN version: with Hyperstack one gets in composite mode 3 images in black and white LUT from which the path to a single RGB image is arduous to the very least (e.g. I did not find it).
>
> Or, using a custom mode one then needs to apply an RGB LUT, then transform in Composite, and finally in RGB to get things OK.
>
> Does anyone have a solution - it would help a lot !
>
> Thanks !
>
> Have a good day !
>
> Pierre
>
> --
> Pierre Godement
> Institut de Genomique Fonctionnelle de Lyon
> UMR 5242 du CNRS
> Ecole Normale Superieure de Lyon
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> France
> Tel: 33 (0)4 26 73 13 21
> Fax: 33 (0)4 26 73 13 75
> E-mail:
> Pierre.Godement at ens-lyon.fr
>
>
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