[ome-users] ome-users Digest, Vol 146, Issue 15//open Carl Zeiss 2011 .czi files of transmitted light images correctly

Tue May 30 15:38:29 BST 2017

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:
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> 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 [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
>> 
>> 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
>> _______________________________________________
>> 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
> 
> ------------------------------
> 
> 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
> ******************************************

Links:
------
[1] https://jenkins.io/security/advisory/2017-04-26/
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