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

Mon Jun 5 14:50:06 BST 2017

Hi Pierre,

Our apologies for the slow response, we were extremely busy with the annual OME Users meeting last week.
Thank you also for submitting the sample file, I was able to test it this morning and could indeed verify the behaviour you had described with the latest Bio-Formats release.

I have created a card to detail this issue on the Bio-Formats Trello board. You can follow any updates to it at the link below:
https://trello.com/c/uhSTHQyV/144-zeiss-czi---2011-images-display-incorrectly

With Thanks,
David Gault

> On 30 May 2017, at 15:38, Godement Pierre <pierre.godement at ens-lyon.fr> wrote:
>
> Hi
>
> So I uploaded an image file (fond clair zeiss 40x 17 ms) via the link provided, https://www.openmicroscopy.org/qa2/qa/upload/
>
> Hope it worked, I could not log in OMERO though I thought I was registered
>
> Thanks
>
> Pierre
>
> --
> Pierre Godement
> Institut de Genomique Fonctionnelle de Lyon
> UMR 5242 du CNRS
> Ecole Normale Superieure de Lyon
> 46, Allee d'Italie
> 69364 Lyon Cedex 07
> 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
>
>
> ------------------------------------------------------
>
> Mailing address:
>
> 46 Allee d'Italie
> 69364 Lyon cedex 07
>
> The IGFL is now located at:
> 32-34 Avenue Tony Garnier, Lyon 69007
>
> For deliveries:
> 29 rue Alexander Fleming, Lyon 69007
>
>
>
> Le 30/05/2017 13:00, ome-users-request at lists.openmicroscopy.org.uk a écrit :
>
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>> Today's Topics:
>>
>>    1. Re: Jenkins downtime due to secvuln (Sebastien Besson (Staff))
>>    2. open Carl Zeiss 2011 .czi files of transmitted light    images
>>       correctly (Godement Pierre)
>>    3. Re: open Carl Zeiss 2011 .czi files of transmitted    light
>>       images correctly (David Gault (Staff))
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Mon, 29 May 2017 12:40:33 +0000
>> From: "Sebastien Besson (Staff)" <s.besson at dundee.ac.uk>
>> To: users OME <ome-users at lists.openmicroscopy.org.uk>
>> Subject: Re: [ome-users] Jenkins downtime due to secvuln
>> Message-ID: <9467DB7F-5841-47C0-8072-9EFE92FDCA79 at dundee.ac.uk>
>> Content-Type: text/plain; charset="utf-8"
>>
>> Dear all,
>>
>> following our email from last month, we wanted to notify you that our Continuous Integration
>> server has been successfully upgraded to the latest LTS version and is now available
>> online again.
>>
>> We thank you for your patience. Please let us know of any issue,
>> The OME Team
>>
>>> On 28 Apr 2017, at 18:14, Kenneth Gillen (Staff) <k.h.gillen at dundee.ac.uk> wrote:
>>>
>>> All,
>>>
>>> A sizable number of security vulnerabilities have recently been released
>>> for Jenkins [1]. This is the software that runs
>>> https://ci.openmicroscopy.org, our public continuous integration server.
>>> Until the system can be upgraded and re-tested, we have taken it offline.
>>> If you have any concerns or difficulty before it comes back online, don?t
>>> hesitate to get in touch with us via the forum or mailing lists
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>>> Otherwise, we apologize for the hassle and thank you for your
>>> understanding.
>>> The OME Team.
>>>
>>> [1] https://jenkins.io/security/advisory/2017-04-26/
>>>
>>>
>>> The University of Dundee is a registered Scottish Charity, No: SC015096
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>>
>> ------------------------------
>>
>> Message: 2
>> Date: Mon, 29 May 2017 18:33:40 +0200
>> From: Godement Pierre <pierre.godement at ens-lyon.fr>
>> To: ome-users at lists.openmicroscopy.org.uk
>> Subject: [ome-users] open Carl Zeiss 2011 .czi files of transmitted
>>     light    images correctly
>> Message-ID: <a7baa63ddbb1b2ea6b3d05813a1ef8c1 at ens-lyon.fr>
>> Content-Type: text/plain; charset="us-ascii"
>>
>> 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
>> 46, Allee d'Italie
>> 69364 Lyon Cedex 07
>> 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
>>
>> ------------------------------------------------------
>>
>> Mailing address:
>>
>> 46 Allee d'Italie
>> 69364 Lyon cedex 07
>>
>> The IGFL is now located at:
>> 32-34 Avenue Tony Garnier, Lyon 69007
>>
>> For deliveries:
>> 29 rue Alexander Fleming, Lyon 69007
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>> ------------------------------
>>
>> Message: 3
>> Date: Tue, 30 May 2017 10:14:55 +0000
>> From: "David Gault (Staff)" <d.gault at dundee.ac.uk>
>> To: OME User Support List <ome-users at lists.openmicroscopy.org.uk>
>> Subject: Re: [ome-users] open Carl Zeiss 2011 .czi files of
>>     transmitted    light    images correctly
>> Message-ID: <EAC75C8E-D741-4D35-B23B-5D441128F62D at dundee.ac.uk>
>> Content-Type: text/plain; charset="us-ascii"
>>
>> 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
>>> 46, Allee d'Italie
>>> 69364 Lyon Cedex 07
>>> 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
>>>
>>>
>>> ------------------------------------------------------
>>>
>>> Mailing address:
>>>
>>> 46 Allee d'Italie
>>> 69364 Lyon cedex 07
>>>
>>> The IGFL is now located at:
>>> 32-34 Avenue Tony Garnier, Lyon 69007
>>>
>>> For deliveries:
>>> 29 rue Alexander Fleming, Lyon 69007
>>>
>>> _______________________________________________
>>> ome-users mailing list
>>> ome-users at lists.openmicroscopy.org.uk
>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>
>>
>> The University of Dundee is a registered Scottish Charity, No: SC015096
>>
>>
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>> End of ome-users Digest, Vol 146, Issue 15
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The University of Dundee is a registered Scottish Charity, No: SC015096