[ome-users] Tile imaging position form lif or czi files
ImageJ
imagejlyd at gmail.com
Fri Feb 20 16:57:33 GMT 2015
Dear LOCI Team,
I’m working on confocal tile imaging on either Leica or Zeiss confocal microscope,
and I was wondering if it was possible to retrieve from .lif or .czi files the X,Y,Z position of the different
individual pictures present in a mosaic sequence ? Actually I looked for it in the OME metadata, but I couldn’ find it.
Am I wrong, or would it be possible ?
Thanks a lot for your help.
Lydia
Lydia Danglot, PhD
Inserm researcher (CR1)
National Research Group on Microscopy (GDR 2588-MIV)
National Coordinator of the France Bio Imaging User committee
--
Institut Jacques Monod (CNRS UMR7592)
Université Paris Diderot
Inserm 950, "Membrane trafic in
Heath & Disease"
Bât.Buffon - 15 rue Hélène Brion
3eme etage, porte 320B
75205 PARIS CEDEX 13 - FRANCE
Tel: 01 57 27 80 37
Site web : http://lydia.danglot.free.fr
Le 20 févr. 2015 à 13:00, ome-users-request at lists.openmicroscopy.org.uk a écrit :
> Send ome-users mailing list submissions to
> ome-users at lists.openmicroscopy.org.uk
>
> To subscribe or unsubscribe via the World Wide Web, visit
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
> or, via email, send a message with subject or body 'help' to
> ome-users-request at lists.openmicroscopy.org.uk
>
> You can reach the person managing the list at
> ome-users-owner at lists.openmicroscopy.org.uk
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of ome-users digest..."
>
>
> Today's Topics:
>
> 1. Re: Omero server installation error: Insight login failure
> (Kenneth Gillen (Staff))
> 2. Re: Omero server installation error: Insight login failure
> (Josh Moore)
> 3. Re: Omero server installation error: Insight login failure
> (Kieran McGourty)
> 4. Re: Omero server installation error: Insight login failure
> (Kieran McGourty)
> 5. Re: Omero server installation error: Insight login failure
> (Kieran McGourty)
> 6. Re: Swap dimensions in OMERO (time vs. z) (Melissa Linkert)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 19 Feb 2015 14:00:31 +0000
> From: "Kenneth Gillen (Staff)" <k.h.gillen at dundee.ac.uk>
> To: "ome-users at lists.openmicroscopy.org.uk"
> <ome-users at lists.openmicroscopy.org.uk>
> Subject: Re: [ome-users] Omero server installation error: Insight
> login failure
> Message-ID: <D10B9BAD.3ACEA%k.h.gillen at dundee.ac.uk>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi Kieran,
>
>> I am trying to install OMERO.server on a windows 7 PC
>
> You?ve likely planned this well already, but I?d just like to mention it
> just anyway: If you?re using a lab PC to host an OMERO server, take care
> to have that PC?s OMERO database and binary repository backed up by your
> institution?s backup system.
>
> All the best with your deployment!
>
> Best,
>
> Kenny
>
> --
>
> Kenneth Gillen
>
> OME System Administrator
>
> Wellcome Trust Centre for Gene Regulation & Expression
> College of Life Sciences
> MSI/WTB/JBC Complex
> University of Dundee
> Dow Street
> Dundee DD1 5EH
> United Kingdom
>
> Tel: +44 (0) 1382 386364
> Skype: kennethgillen
>
> http://www.twitter.com/openmicroscopy
>
>
>
>
>
> From: Kieran McGourty <kieran.mcgourty at gmail.com>
> Reply-To: "ome-users at lists.openmicroscopy.org.uk"
> <ome-users at lists.openmicroscopy.org.uk>
> Date: Thursday, 19 February 2015 00:36
> To: "ome-users at lists.openmicroscopy.org.uk"
> <ome-users at lists.openmicroscopy.org.uk>
> Subject: [ome-users] Omero server installation error: Insight login
> failure
>
>
> Hello OMERO users,
> I'm not sure you are the correct people to speak to on this but I have
> searched and have come up blank on what to do next so I thought I would
> ask you.
>
> I am trying to install OMERO.server on a windows 7 PC that we have in the
> lab. Ideally I would take image data acquired on an ImageXpress on a HDD
> and load them locally onto the OMERO server to store and process.
> Potentially
> with cell profiler and cell profiler analyst( if I can get them working).
> I have followed the installation procedure for the OMERO server and
> everything worked up until the point where I try to login with the insight
> client or via the CMD prompt. It tells
> me my username or password are incorrect.
>
> I have attached my server diagnostics. I hope you are able to help with
> this as I think it will be absolutely ideal for our purposes.
>
> Also, I am running the server software on the same machine I am trying to
> run insight on. That should not make a difference right?
> Interestingly, I can get the webclient using the VM build of OMERO working
> but not through insight. Finally, I can successfully connect to the demo
> server using insight.
>
> Thanks a lot for your time all,
>
> All the best,
>
> Kieran
>
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
>
>
> ------------------------------
>
> Message: 2
> Date: Thu, 19 Feb 2015 15:34:15 +0100
> From: Josh Moore <josh at glencoesoftware.com>
> To: OME User Support List <ome-users at lists.openmicroscopy.org.uk>
> Subject: Re: [ome-users] Omero server installation error: Insight
> login failure
> Message-ID:
> <CAD3Ea=UuGqcWAYkWJz+A5CzU_V-dZvmoN_aDG_oao0wUTXLF9A at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi Kieran,
>
> On Thu, Feb 19, 2015 at 12:48 PM, Kieran McGourty
> <kieran.mcgourty at gmail.com> wrote:
>> OK great. Almost there. I created some users of all types in the root login
>> in insight. I was then able to successfully login from both the server
>> machine and another computer on the same network!! Thanks a lot! Success :-)
>>
>> Then I went add my first sample tiff via importer. using a user login, a
>> administrator login and a root login from insight running on the server
>> machine. The import failed each time. Not sure why. I have attached the
>> insight log to this email.
>
> Thanks, but there doesn't seem to be anything in the log related to
> your import. Can you submit an error report for the failed import?
>
> Cheers,
> ~Josh.
>
>
>> Thanks a lot again Josh.
>>
>> So close now...
>>
>> On 19 February 2015 at 10:08, Josh Moore <josh at glencoesoftware.com> wrote:
>>>
>>> On Thu, Feb 19, 2015 at 11:03 AM, Kieran McGourty
>>> <kieran.mcgourty at gmail.com> wrote:
>>>> Hello Josh,
>>>
>>> Hi,
>>>
>>>
>>>> Thank you so much for the excellent support. I have taken on your
>>>> suggestion
>>>> and have had some success.
>>>>
>>>> I can login bin\omero login root at localhost
>>>>
>>>> I can also login to insight at under the root root account.
>>>
>>> Alright, that sounds very promising. As what user are you trying to
>>> login as now?
>>>
>>> After bin\omero login root at localhost, you might try:
>>>
>>> bin\omero user list
>>>
>>>
>>> Those are the other users on your system. If you were expecting more,
>>> then you'll either need to add them via:
>>>
>>> bin\omero user add -h
>>>
>>>
>>> Or enable LDAP.
>>>
>>>> ...
>>>> Thanks a lot again for the amazing support.
>>>
>>> Gladly!
>>> ~Josh.
>>>
>>>
>>>> Kieran
>>>>
>>>>
>>>> On 19 February 2015 at 07:25, Josh Moore <josh at glencoesoftware.com>
>>>> wrote:
>>>>>
>>>>> On Thu, Feb 19, 2015 at 1:36 AM, Kieran McGourty
>>>>> <kieran.mcgourty at gmail.com> wrote:
>>>>>> Hello OMERO users,
>>>>>
>>>>> Hi Kieran,
>>>>>
>>>>>
>>>>>> I'm not sure you are the correct people to speak to on this but I
>>>>>> have
>>>>>> searched and have come up blank on what to do next so I thought I
>>>>>> would
>>>>>> ask
>>>>>> you.
>>>>>
>>>>> This is just the spot. Hopefully we can help.
>>>>>
>>>>>
>>>>>> I am trying to install OMERO.server on a windows 7 PC that we have in
>>>>>> the
>>>>>> lab. Ideally I would take image data acquired on an ImageXpress on a
>>>>>> HDD
>>>>>> and
>>>>>> load them locally onto the OMERO server to store and process.
>>>>>> Potentially
>>>>>> with cell profiler and cell profiler analyst( if I can get them
>>>>>> working). I
>>>>>> have followed the installation procedure for the OMERO server and
>>>>>> everything
>>>>>> worked up until the point where I try to login with the insight
>>>>>> client
>>>>>> or
>>>>>> via the CMD prompt. It tells me my username or password are
>>>>>> incorrect.
>>>>>> I have attached my server diagnostics.
>>>>>
>>>>>
>>>>> Your diagnosis output generally looks ok, i.e. the server is running.
>>>>> If you could also send us the Blitz-0.log, there seem to be a number
>>>>> errors:
>>>>>
>>>>> Log files: Blitz-0.log 568.0 KB errors=33 warnings=90
>>>>>
>>>>> This might just be caused by previous configuration attempts. Have you
>>>>> tried logging in from the command-line yet?
>>>>>
>>>>> bin\omero login root at localhost
>>>>>
>>>>>
>>>>>
>>>>>> Also, I am running the server software on the same machine I am
>>>>>> trying
>>>>>> to
>>>>>> run insight on. That should not make a difference right?
>>>>>
>>>>> There shouldn't be any problem doing that, and we certainly all do it
>>>>> for testing. Eventually, you will want to have the server safely
>>>>> behind a firewall though.
>>>>>
>>>>>
>>>>>> Interestingly, I can get the webclient using the VM build of OMERO
>>>>>> working
>>>>>> but not through insight. Finally, I can successfully connect to the
>>>>>> demo
>>>>>> server using insight.
>>>>>
>>>>> That is interesting. Hopefully a good sign, though, that most of the
>>>>> pieces are working, and we just have to figure out what's gona awry
>>>>> with your Windows installation.
>>>>>
>>>>>
>>>>>> Thanks a lot for your time all,
>>>>>>
>>>>>> All the best,
>>>>>> Kieran
>>>>>
>>>>> Cheers,
>>>>> ~Josh
>
>
> ------------------------------
>
> Message: 3
> Date: Thu, 19 Feb 2015 17:37:52 +0000
> From: Kieran McGourty <kieran.mcgourty at gmail.com>
> To: OME User Support List <ome-users at lists.openmicroscopy.org.uk>
> Subject: Re: [ome-users] Omero server installation error: Insight
> login failure
> Message-ID:
> <CACVYweqt_ncFHjuP7G=S76E4KpVrjE-RZGuxzj7vNNxh8NsYPQ at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hey Josh,
>
> Success!
>
> I think I figured it out... well under guidance. Import was looking for a
> .hdt file which contains the metadata from the ImageExpress export in the
> folder that I was uploading the images from. When I moved any one of the
> images out of that folder they uploaded fine. Conveniently, when I only
> selected the .hdt file it uploaded the full set of images in the folder. (I
> guess what it was designed to do)
>
> In summary, amazing software with fantastic support.
>
> Thanks a lot for your help.
>
> Kieran
>
> p.s. now... to interface Cellprofiler and Cellanalayst. Tomorrows puzzle!!!
>
>
>
>
>
> On 19 February 2015 at 14:34, Josh Moore <josh at glencoesoftware.com> wrote:
>
>> Hi Kieran,
>>
>> On Thu, Feb 19, 2015 at 12:48 PM, Kieran McGourty
>> <kieran.mcgourty at gmail.com> wrote:
>>> OK great. Almost there. I created some users of all types in the root
>> login
>>> in insight. I was then able to successfully login from both the server
>>> machine and another computer on the same network!! Thanks a lot! Success
>> :-)
>>>
>>> Then I went add my first sample tiff via importer. using a user login, a
>>> administrator login and a root login from insight running on the server
>>> machine. The import failed each time. Not sure why. I have attached the
>>> insight log to this email.
>>
>> Thanks, but there doesn't seem to be anything in the log related to
>> your import. Can you submit an error report for the failed import?
>>
>> Cheers,
>> ~Josh.
>>
>>
>>> Thanks a lot again Josh.
>>>
>>> So close now...
>>>
>>> On 19 February 2015 at 10:08, Josh Moore <josh at glencoesoftware.com>
>> wrote:
>>>>
>>>> On Thu, Feb 19, 2015 at 11:03 AM, Kieran McGourty
>>>> <kieran.mcgourty at gmail.com> wrote:
>>>>> Hello Josh,
>>>>
>>>> Hi,
>>>>
>>>>
>>>>> Thank you so much for the excellent support. I have taken on your
>>>>> suggestion
>>>>> and have had some success.
>>>>>
>>>>> I can login bin\omero login root at localhost
>>>>>
>>>>> I can also login to insight at under the root root account.
>>>>
>>>> Alright, that sounds very promising. As what user are you trying to
>>>> login as now?
>>>>
>>>> After bin\omero login root at localhost, you might try:
>>>>
>>>> bin\omero user list
>>>>
>>>>
>>>> Those are the other users on your system. If you were expecting more,
>>>> then you'll either need to add them via:
>>>>
>>>> bin\omero user add -h
>>>>
>>>>
>>>> Or enable LDAP.
>>>>
>>>>> ...
>>>>> Thanks a lot again for the amazing support.
>>>>
>>>> Gladly!
>>>> ~Josh.
>>>>
>>>>
>>>>> Kieran
>>>>>
>>>>>
>>>>> On 19 February 2015 at 07:25, Josh Moore <josh at glencoesoftware.com>
>>>>> wrote:
>>>>>>
>>>>>> On Thu, Feb 19, 2015 at 1:36 AM, Kieran McGourty
>>>>>> <kieran.mcgourty at gmail.com> wrote:
>>>>>>> Hello OMERO users,
>>>>>>
>>>>>> Hi Kieran,
>>>>>>
>>>>>>
>>>>>>> I'm not sure you are the correct people to speak to on this but I
>>>>>>> have
>>>>>>> searched and have come up blank on what to do next so I thought I
>>>>>>> would
>>>>>>> ask
>>>>>>> you.
>>>>>>
>>>>>> This is just the spot. Hopefully we can help.
>>>>>>
>>>>>>
>>>>>>> I am trying to install OMERO.server on a windows 7 PC that we have
>> in
>>>>>>> the
>>>>>>> lab. Ideally I would take image data acquired on an ImageXpress on
>> a
>>>>>>> HDD
>>>>>>> and
>>>>>>> load them locally onto the OMERO server to store and process.
>>>>>>> Potentially
>>>>>>> with cell profiler and cell profiler analyst( if I can get them
>>>>>>> working). I
>>>>>>> have followed the installation procedure for the OMERO server and
>>>>>>> everything
>>>>>>> worked up until the point where I try to login with the insight
>>>>>>> client
>>>>>>> or
>>>>>>> via the CMD prompt. It tells me my username or password are
>>>>>>> incorrect.
>>>>>>> I have attached my server diagnostics.
>>>>>>
>>>>>>
>>>>>> Your diagnosis output generally looks ok, i.e. the server is running.
>>>>>> If you could also send us the Blitz-0.log, there seem to be a number
>>>>>> errors:
>>>>>>
>>>>>> Log files: Blitz-0.log 568.0 KB errors=33 warnings=90
>>>>>>
>>>>>> This might just be caused by previous configuration attempts. Have
>> you
>>>>>> tried logging in from the command-line yet?
>>>>>>
>>>>>> bin\omero login root at localhost
>>>>>>
>>>>>>
>>>>>>
>>>>>>> Also, I am running the server software on the same machine I am
>>>>>>> trying
>>>>>>> to
>>>>>>> run insight on. That should not make a difference right?
>>>>>>
>>>>>> There shouldn't be any problem doing that, and we certainly all do it
>>>>>> for testing. Eventually, you will want to have the server safely
>>>>>> behind a firewall though.
>>>>>>
>>>>>>
>>>>>>> Interestingly, I can get the webclient using the VM build of OMERO
>>>>>>> working
>>>>>>> but not through insight. Finally, I can successfully connect to the
>>>>>>> demo
>>>>>>> server using insight.
>>>>>>
>>>>>> That is interesting. Hopefully a good sign, though, that most of the
>>>>>> pieces are working, and we just have to figure out what's gona awry
>>>>>> with your Windows installation.
>>>>>>
>>>>>>
>>>>>>> Thanks a lot for your time all,
>>>>>>>
>>>>>>> All the best,
>>>>>>> Kieran
>>>>>>
>>>>>> Cheers,
>>>>>> ~Josh
>> _______________________________________________
>> ome-users mailing list
>> ome-users at lists.openmicroscopy.org.uk
>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20150219/159b9ab1/attachment-0001.html>
>
> ------------------------------
>
> Message: 4
> Date: Thu, 19 Feb 2015 17:45:01 +0000
> From: Kieran McGourty <kieran.mcgourty at gmail.com>
> To: OME User Support List <ome-users at lists.openmicroscopy.org.uk>
> Subject: Re: [ome-users] Omero server installation error: Insight
> login failure
> Message-ID:
> <CACVYweqN0xYnVSL+_98rPrPU80zpAtD+S4R3aNMV5cNGFcUdtQ at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hello Kenny,
>
> Thanks a lot for the advice. I are going to go shopping for a mini server
> here and a QNAP NAS system for local backup. I explored setting something
> up here in UCL with our IT team but they said that there systems were not
> really designed for suck large amounts of data. It is cheaper to get a
> bumbler like me to try and set one up that I manage myself.
>
> Thanks so much for your time. It is a great community.
>
> All the best,
>
> Kieran
>
> On 19 February 2015 at 14:00, Kenneth Gillen (Staff) <
> k.h.gillen at dundee.ac.uk> wrote:
>
>> Hi Kieran,
>>
>>> I am trying to install OMERO.server on a windows 7 PC
>>
>> You?ve likely planned this well already, but I?d just like to mention it
>> just anyway: If you?re using a lab PC to host an OMERO server, take care
>> to have that PC?s OMERO database and binary repository backed up by your
>> institution?s backup system.
>>
>> All the best with your deployment!
>>
>> Best,
>>
>> Kenny
>>
>> --
>>
>> Kenneth Gillen
>>
>> OME System Administrator
>>
>> Wellcome Trust Centre for Gene Regulation & Expression
>> College of Life Sciences
>> MSI/WTB/JBC Complex
>> University of Dundee
>> Dow Street
>> Dundee DD1 5EH
>> United Kingdom
>>
>> Tel: +44 (0) 1382 386364
>> Skype: kennethgillen
>>
>> http://www.twitter.com/openmicroscopy
>>
>>
>>
>>
>>
>> From: Kieran McGourty <kieran.mcgourty at gmail.com>
>> Reply-To: "ome-users at lists.openmicroscopy.org.uk"
>> <ome-users at lists.openmicroscopy.org.uk>
>> Date: Thursday, 19 February 2015 00:36
>> To: "ome-users at lists.openmicroscopy.org.uk"
>> <ome-users at lists.openmicroscopy.org.uk>
>> Subject: [ome-users] Omero server installation error: Insight login
>> failure
>>
>>
>> Hello OMERO users,
>> I'm not sure you are the correct people to speak to on this but I have
>> searched and have come up blank on what to do next so I thought I would
>> ask you.
>>
>> I am trying to install OMERO.server on a windows 7 PC that we have in the
>> lab. Ideally I would take image data acquired on an ImageXpress on a HDD
>> and load them locally onto the OMERO server to store and process.
>> Potentially
>> with cell profiler and cell profiler analyst( if I can get them working).
>> I have followed the installation procedure for the OMERO server and
>> everything worked up until the point where I try to login with the insight
>> client or via the CMD prompt. It tells
>> me my username or password are incorrect.
>>
>> I have attached my server diagnostics. I hope you are able to help with
>> this as I think it will be absolutely ideal for our purposes.
>>
>> Also, I am running the server software on the same machine I am trying to
>> run insight on. That should not make a difference right?
>> Interestingly, I can get the webclient using the VM build of OMERO working
>> but not through insight. Finally, I can successfully connect to the demo
>> server using insight.
>>
>> Thanks a lot for your time all,
>>
>> All the best,
>>
>> Kieran
>>
>>
>> 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
>>
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20150219/fc9da4b3/attachment-0001.html>
>
> ------------------------------
>
> Message: 5
> Date: Thu, 19 Feb 2015 17:48:52 +0000
> From: Kieran McGourty <kieran.mcgourty at gmail.com>
> To: OME User Support List <ome-users at lists.openmicroscopy.org.uk>
> Subject: Re: [ome-users] Omero server installation error: Insight
> login failure
> Message-ID:
> <CACVYwepJAhF_Mys5s+T3H2se-iGEVEDYiVzRx0NY5i-GVCJY9A at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> *we and *such
>
> On 19 February 2015 at 17:45, Kieran McGourty <kieran.mcgourty at gmail.com>
> wrote:
>
>> Hello Kenny,
>>
>> Thanks a lot for the advice. I are going to go shopping for a mini server
>> here and a QNAP NAS system for local backup. I explored setting something
>> up here in UCL with our IT team but they said that there systems were not
>> really designed for suck large amounts of data. It is cheaper to get a
>> bumbler like me to try and set one up that I manage myself.
>>
>> Thanks so much for your time. It is a great community.
>>
>> All the best,
>>
>> Kieran
>>
>> On 19 February 2015 at 14:00, Kenneth Gillen (Staff) <
>> k.h.gillen at dundee.ac.uk> wrote:
>>
>>> Hi Kieran,
>>>
>>>> I am trying to install OMERO.server on a windows 7 PC
>>>
>>> You?ve likely planned this well already, but I?d just like to mention it
>>> just anyway: If you?re using a lab PC to host an OMERO server, take care
>>> to have that PC?s OMERO database and binary repository backed up by your
>>> institution?s backup system.
>>>
>>> All the best with your deployment!
>>>
>>> Best,
>>>
>>> Kenny
>>>
>>> --
>>>
>>> Kenneth Gillen
>>>
>>> OME System Administrator
>>>
>>> Wellcome Trust Centre for Gene Regulation & Expression
>>> College of Life Sciences
>>> MSI/WTB/JBC Complex
>>> University of Dundee
>>> Dow Street
>>> Dundee DD1 5EH
>>> United Kingdom
>>>
>>> Tel: +44 (0) 1382 386364
>>> Skype: kennethgillen
>>>
>>> http://www.twitter.com/openmicroscopy
>>>
>>>
>>>
>>>
>>>
>>> From: Kieran McGourty <kieran.mcgourty at gmail.com>
>>> Reply-To: "ome-users at lists.openmicroscopy.org.uk"
>>> <ome-users at lists.openmicroscopy.org.uk>
>>> Date: Thursday, 19 February 2015 00:36
>>> To: "ome-users at lists.openmicroscopy.org.uk"
>>> <ome-users at lists.openmicroscopy.org.uk>
>>> Subject: [ome-users] Omero server installation error: Insight login
>>> failure
>>>
>>>
>>> Hello OMERO users,
>>> I'm not sure you are the correct people to speak to on this but I have
>>> searched and have come up blank on what to do next so I thought I would
>>> ask you.
>>>
>>> I am trying to install OMERO.server on a windows 7 PC that we have in the
>>> lab. Ideally I would take image data acquired on an ImageXpress on a HDD
>>> and load them locally onto the OMERO server to store and process.
>>> Potentially
>>> with cell profiler and cell profiler analyst( if I can get them working).
>>> I have followed the installation procedure for the OMERO server and
>>> everything worked up until the point where I try to login with the insight
>>> client or via the CMD prompt. It tells
>>> me my username or password are incorrect.
>>>
>>> I have attached my server diagnostics. I hope you are able to help with
>>> this as I think it will be absolutely ideal for our purposes.
>>>
>>> Also, I am running the server software on the same machine I am trying to
>>> run insight on. That should not make a difference right?
>>> Interestingly, I can get the webclient using the VM build of OMERO working
>>> but not through insight. Finally, I can successfully connect to the demo
>>> server using insight.
>>>
>>> Thanks a lot for your time all,
>>>
>>> All the best,
>>>
>>> Kieran
>>>
>>>
>>> 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
>>>
>>
>>
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20150219/a84b0c3c/attachment-0001.html>
>
> ------------------------------
>
> Message: 6
> Date: Thu, 19 Feb 2015 12:18:46 -0600
> From: Melissa Linkert <melissa at glencoesoftware.com>
> To: Niko Ehrenfeuchter <nikolaus.ehrenfeuchter at unibas.ch>
> Cc: OME User Support List <ome-users at lists.openmicroscopy.org.uk>
> Subject: Re: [ome-users] Swap dimensions in OMERO (time vs. z)
> Message-ID: <20150219181846.GA12235 at hera>
> Content-Type: text/plain; charset=us-ascii
>
> Hi Niko,
>
>> I just re-imported it, the log file is attached.
>
> According to the metadata in the original .nd file, there should be 3
> channels and 5 Z sections. That is what I see when importing either the
> .nd or one or the .stk files into a 5.0.8 server. If you open the .nd
> file in a text editor, it should show that "NZSteps" is set to 5 and
> "DoTimelapse" is set to false.
>
> Does the acquisition software show 5 timepoints? That would definitely
> worry me; probably the easiest thing for us to do in that case is to
> update the reader to change dimensions based upon the recorded acquisition software.
>
>>>> On top of that we have some more (non-Visitron) Metamorph TIFFs which have
>>>> their T interpreted as Z and their C as T. I can upload one of these,
>>>> although the smallest one that I have is ~850 MB. Inspecting the metadata
>>>> with Fiji shows the expected odd inconsistency on those, stating the images
>>>> should have 2 timepoints (instead of the real 165), but then giving T x C
>>>> "timepoints" further down.
>>>>
>>>> Don't know if this is a related issue though. Let me know if I should upload
>>>> it!
>>>
>>> I'll defer to Melissa on that.
>
> http://trac.openmicroscopy.org/ome/ticket/12503 is likely related if an
> .nd file is not present. It would help to have the file if you don't
> mind, and we'll certainly do our best - reliably determining the
> dimensions for Metamorph TIFFs (especially distinguishing between Z and
> T) is notoriously tricky though, so it may not be 100%.
>
> Regards,
> -Melissa
>
> On Thu, Feb 19, 2015 at 12:36:53PM +0100, Niko Ehrenfeuchter wrote:
>> Hi Josh,
>>
>> On 18.02.2015 20:40, Josh Moore wrote:
>>>> Otherwise I can also dig through the logs here, I guess you're asking for
>>>> the Blitz-0.log?
>>>
>>> Nope, I mean the log file which sits beside the fileset under
>>> ManagedRepository. For example, for
>>>
>>> # jamoore at joshuas-mbp:/opt/ome6$ dist/bin/omero -q fs sets
>>> # | Id | Prefix | Images | Files | Transfer
>>> ---+-----+---------------------------------+--------+-------+----------
>>> 0 | 301 | root_0/2015-02/18/10-27-33.022/ | 1 | 1 |
>>> 1 | 251 | root_0/2015-02/18/10-20-40.871/ | 1 | 1 |
>>> 2 | 202 | root_0/2015-02/18/10-01-20.181/ | 1 | 1 |
>>> 3 | 201 | root_0/2015-02/18/10-01-02.432/ | 1 | 1 |
>>> (4 rows, starting at 0 of approx. 4)
>>> # jamoore at joshuas-mbp:/opt/ome6$ dist/bin/omero hql "select
>>> f.templatePrefix from Image i join i.fileset as f where i.id = 251" -q
>>> # | Col1
>>> ---+---------------------------------
>>> 0 | root_0/2015-02/18/10-20-40.871/
>>> (1 row)
>>>
>>> the log file would be found under
>>>
>>> /OMERO/ManagedRepository/root_0/2015-02/18/10-20-40.871.log
>>
>> I just re-imported it, the log file is attached.
>>
>>
>>>> On top of that we have some more (non-Visitron) Metamorph TIFFs which have
>>>> their T interpreted as Z and their C as T. I can upload one of these,
>>>> although the smallest one that I have is ~850 MB. Inspecting the metadata
>>>> with Fiji shows the expected odd inconsistency on those, stating the images
>>>> should have 2 timepoints (instead of the real 165), but then giving T x C
>>>> "timepoints" further down.
>>>>
>>>> Don't know if this is a related issue though. Let me know if I should upload
>>>> it!
>>>
>>> I'll defer to Melissa on that.
>>
>> Alright, I'll happily wait then :-)
>>
>> Cheers,
>> ~Niko
>
>
>> _______________________________________________
>> ome-users mailing list
>> ome-users at lists.openmicroscopy.org.uk
>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
>
>
> ------------------------------
>
> Subject: Digest Footer
>
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
>
> ------------------------------
>
> End of ome-users Digest, Vol 119, Issue 23
> ******************************************
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20150220/64f16ea9/attachment.html>
More information about the ome-users
mailing list