[ome-users] opening czi files.

Mon May 23 12:02:16 BST 2016

Thanks for the fast action, hope it helps also other users in the end.

Regards

Raphael COURJARET
Research Associate
Research Department
Weill Cornell Medicine - Qatar
Qatar Foundation -Education City
P.O.Box  24144
DOHA - STATE OF QATAR
Tel   +974 4492 8453
Mob +974 3347 5013
Fax  +974 4492 8422
rac2017 at qatar-med.cornell.edu

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Today's Topics:

   1. Re: opening czi files. (Balaji Ramalingam (Staff))
   2. Re: Group mapping (LDAP) (Aleksandra Tarkowska (Staff))
   3. Re: Group mapping (LDAP) (Shaun Hare)

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Message: 1
Date: Mon, 23 May 2016 08:18:24 +0000
From: "Balaji Ramalingam (Staff)" <b.ramalingam at dundee.ac.uk>
To: OME User Support List <ome-users at lists.openmicroscopy.org.uk>
Subject: Re: [ome-users] opening czi files.
Message-ID: <D3687AC2.1EC42%b.ramalingam at dundee.ac.uk>
Content-Type: text/plain; charset="Windows-1252"

Hi,

Thank you for submitting your files.
We were able to reproduce the issue on one of the files ?Conv 2 3 colors?, using Bio-Formats 5.1.9 on FIJI.

I have filed a ticket on this regard,
https://trac.openmicroscopy.org/ome/ticket/13239

This will get looked into at the earliest.
I have also added you to the CC list and you will get notified when there is a status change on the ticket.

Hope that helps.

Best,
Balaji
__________________
Mr Balaji Ramalingam
Software Developer

OME Team
College of Life Sciences
University of Dundee

On 18/05/2016 08:58, "Raphael J. Courjaret"
<rac2017 at qatar-med.cornell.edu> wrote:

>Hi and thanks for the reply.
>I uploaded three files in czi format.
>Strangely now none of them open after updating FIJI...
>
>Conv 2 3 colors BandW
>Conv 2 3 colors
>Convalaria 2 channels
>
>They are listed in the software as 36 bits for the RGB ones and 12 bits 
>for the B&W...
>When FIJI opened some they were declared as 16bits...?
>
>Regards
>
>Raphael COURJARET
>Research Associate
>Research Department
>Weill Cornell Medicine - Qatar
>Qatar Foundation -Education City
>P.O.Box  24144
>DOHA - STATE OF QATAR
>Tel   +974 4492 8453
>Mob +974 3347 5013
>Fax  +974 4492 8422
>rac2017 at qatar-med.cornell.edu
>__________________
>
>Mr Balaji Ramalingam
>
>Software Developer
>
>OME Team
>
>College of Life Sciences
>
>University of Dundee
>
>From: "Raphael J. Courjaret"
><rac2017 at qatar-med.cornell.edu<mailto:rac2017 at qatar-med.cornell.edu>>
>Reply-To: OME User Support List
><ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicro
>sco
>py.org.uk>>
>Date: Tuesday, 17 May 2016 06:37
>To:
>"ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicro
>sco
>py.org.uk>"
><ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicro
>sco
>py.org.uk>>
>Subject: [ome-users] Czi image using Bio-Format/FIJI
>
>Good morning all.
>We are trying to open with FIJI some files that have been produced with 
>Zen Blue and are saved as .czi. Single channel files open well but 
>multi fail to open (36 bits, RVB).
>FIJI and the Bio-format plugin are up to date.
>
>Regards
>
>Raphael COURJARET
>Research Associate
>Research Department
>Weill CornellMedicine- Qatar
>Qatar Foundation -Education City
>P.O.Box  24144
>DOHA - STATE OF QATAR
>Tel   +974 4492 8453
>Mob +974 3347 5013
>Fax  +974 4492 8422
>rac2017 at qatar-med.cornell.edu<mailto:rac2017 at qatar-med.cornell.edu>
>
>
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Message: 2
Date: Mon, 23 May 2016 09:46:56 +0000
From: "Aleksandra Tarkowska (Staff)" <A.Tarkowska at dundee.ac.uk>
To: OME User Support List <ome-users at lists.openmicroscopy.org.uk>
Subject: Re: [ome-users] Group mapping (LDAP)
Message-ID: <1DD952CF-0820-4DD3-995E-C485460AA28C at dundee.ac.uk>
Content-Type: text/plain; charset="utf-8"

Hi Shaun,

What exactly you mean by re-install, did you upgrade?
Could you detail more what is not working exactly, is there any error in Blitz-1.log file?

Could you give us more details about your previous and recent installations, which version did you use before and now, output of:
 - bin/omero config get --hide-password
 - bin/omero admin diagnostics

Could you send example ldap entry of user and group?

Could you try CLI and show the output of:
 - bin/omero ldap active
 - bin/omero ldap discover
 - bin/omero ldap getdn --user-name USERNAME
 - bin/omero login username at server:4064  #please use ldap user

Could you also send all logs stored in /path/to/omero/var/log

If you prefer not to share all the above, please use http://qa.openmicroscopy.org.uk/qa/upload/

From the other hand, did you try `omero.ldap.sync_on_login true` https://www.openmicroscopy.org/site/support/omero5.2/sysadmins/server-ldap.html#synchronizing-ldap-on-user-login

Ola
Software Engineer
Open Microscopy Environment
University of Dundee

On 20 May 2016, at 18:15, Shaun Hare <Shaun.Hare at nottingham.ac.uk<mailto:Shaun.Hare at nottingham.ac.uk>> wrote:

Hi community members

We have previously had configuration working for group mapping here at Nottingham University However after a re-install the settings don?t seem to be working ? could anyone please advise if there is a issue here What we are trying to achieve is new users go into the group they are a member of (note they will belong to many groups) E.g members of cn=LS-OMERO-SRM go into that group

Settings

omero.ldap.base=ou=Users,ou=University,dc=ad,dc=nottingham,dc=ac,dc=uk
omero.ldap.config=true
omero.ldap.group_filter=(|(cn=LS-OMERO-SRM)(cn=LS-OMERO-LSM710))
omero.ldap.group_mapping=name=cn
omero.ldap.new_user_group=:query:(member=@{dn})
omero.ldap.password=********
omero.ldap.urls=*********
omero.ldap.user_filter=(|(memberOf=CN=LS-Omero-SRM,ou=Groups,ou=LS,ou=L,ou=Groups,ou=University,dc=ad,dc=nottingham,dc=ac,dc=uk)(memberOf=CN=LS-Omero-LSM710,ou=Groups,ou=LS,ou=L,ou=Groups,ou=University,dc=ad,dc=nottingham,dc=ac,dc=uk))
omero.ldap.user_mapping=omeName=sAMAccountName,firstName=givenName,lastName=sn,email=mail
omero.ldap.username=CN=*********,CN=Users,DC=ad,DC=nottingham,DC=ac,DC=uk

Many thanks in anticipation

Shaun

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Message: 3
Date: Mon, 23 May 2016 10:10:02 +0000
From: Shaun Hare <Shaun.Hare at nottingham.ac.uk>
To: OME User Support List <ome-users at lists.openmicroscopy.org.uk>
Subject: Re: [ome-users] Group mapping (LDAP)
Message-ID:
	<984324DB-BD93-44E2-8C33-498A8749D642 at exmail.nottingham.ac.uk>
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