Open Microscopy Environment

Hi,

I failed several times to import .TIF images associated with .nd files.
I tried with only the .nd, only .TIF and both together but it always ended in a failure.
Not exactly a failure cause he upload the first time point but fails every other one after.
Also, i cannot access the log since the 2 options are greyed...
Any ideas?
the images come from a film made with a spining disk roper microscope.

Best,

Alex.

Hi Alex,

what version and client are you using? Is there anything in your log file? Or do you get an explicit error message?

Cheers,
~Josh.

Hi,

We are currently working under omero 5.0.5 and we 're waiting for the 5.1 release to update our system.
In Importer, there are no explanations given like i said, just a red cross with failed and i cannot access the log import that is usually available when you click on view.


On a completely different note, we found out that Super Omero lives in our basement, is it Ok if he uses your logo (see attachment)?

Best,

Alex.

LeroyAlex wrote:We are currently working under omero 5.0.5 and we 're waiting for the 5.1 release to update our system.
In Importer, there are no explanations given like i said, just a red cross with failed and i cannot access the log import that is usually available when you click on view.

And in the ~/omero/log/omeroinsight.log file?

On a completely different note, we found out that Super Omero lives in our basement, is it Ok if he uses your logo (see attachment)?

Gladly! Welcome.
~Josh.

Hi,

i m not quite sure how to look at those?

Best,

Alex.

Hi Alex,

unfortunately it turned out, that the Insight log won't be of much help. We'd actually need the import log, which is stored on the server. Could you make another attempt to import the file and note the date and time of this attempt? With this information and your username, your server admin could get the import log associated to this action. It's a log file within your server's managed repository folder, i. e. [path to omero repository]/ManagedRepository/[your username]/[date]/[timestamp].log
If it's possible to get this log file, you could upload it to us via: https://www.openmicroscopy.org/qa2/qa/upload/

Cheers,
Dominik

Hi Alex,

there's another way, you can get the import log file without having administrative access to the omero server. You can use the command line client (which is bundled in the server package), for details see: http://www.openmicroscopy.org/site/supp ... rface.html

In short, you download the 5.0.8 server package, go the bin directory and upload the file again via the command line interface (you'll get asked for the server hostname, login credentials, etc.):

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./omero import [Image file]

In the output you will see a line like this:

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2015-03-31 09:00:44,250 3115       [      main] INFO   ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 26210

Take a note of the log file ID.

Then you can request the log file by:

Code: Select all

./omero download [log file ID] importlog.txt

Hi,

In the import module of OMERO.insight 5.1 the file type list for Metamorph files STK is : *.stk, *.nd, *.tif, *.tiff. However, if the user want to select only nd files it's difficult when the number of associated tif files is important. One suggestion is to have a file type Metamorph with only *.nd and only *.stk, *.tif file is not necessary.


Philippe

thanks for the suggestion, Philippe. I've filed a ticket under http://trac.openmicroscopy.org.uk/ome/ticket/12845

Cheers,
~Josh.