[ome-users] .mrc file import into omero

Fri Jul 10 11:52:21 BST 2009

Dear Brian and Quentin,

So we can safely assume that .mrc file import wont be officially  
supported by OMERO  in the short term,
but it will come eventually.

However, i can look at the .mrc format and see that meta data is there  
and what bio-formats can read,
then maybe hack our omero server so that it will read it in and read  
the meta data.

So then at least there is a test site trying to use .mrc.

If I change the
> importer_readers.txt file
to allow .mrc
will the results of then import make any sense?
Maybe the image data will be ok, but the meta data might be weird?

Or is more work required for that to be somewhat useable?
At least we can help figure out what works and what does not.

Dan

On Jul 10, 2009, at 12:36 PM, Brian Loranger wrote:

> Hi Dan and Bjorn,
>
> OMERO officially only supports about 30 of the Bio-formats file  
> types and the list of those formats can be found at: http://trac.openmicroscopy.org.uk/omero/wiki/ImporterFormats 
>  and is also mentioned in our FAQ at https://www.openmicroscopy.org/site/support/faq 
>  .
>
> The reason for this is primary one of testing - because of the  
> diverse range of metadata that can be included in the various file  
> formats, we're pretty cautious about including everything before we  
> have a chance to test it.
>
> In the past OMERO has been pretty light-microscopy centric, but  
> happily EM data is one of the areas we're now looking at. Some model  
> changes probably need to be made to fully support EM metadata, and I  
> wouldn't expect us to see those formats officially supported till  
> we've gone ahead with those changes.
>
> In the current release of the importer, there's no easy way for the  
> end use to go in and 'turn on' formats for testing, but I've already  
> submitted a change to the source code to allow you to do that in  
> upcoming releases (the required 'importer_readers.txt' file for  
> turning on file formats will be in the importer's config folder). In  
> the mean time, if you're interested in turning on formats, you'll  
> need to extract the importer jar, tweak the importer_readers.txt  
> file, and jar it up again.
>
> I should mention that the process of testing these formats is just  
> that - experimental, and you should probably be familiar with a bit  
> of java code to get things going.
>
> Cheers,
>
> Brian
>
> On 10 Jul 2009, at 11:10, Daniel James White wrote:
>
>> Hi Bjorn,
>>
>> Well, the point is that bio-formats reads the electron microscopy
>> format .mrc
>> but OMERO.import does not.
>>
>> I dont know if its supposed to or not,
>> or if there is some way i can add support by turning it on on the
>> server,
>> or by working out how to do it and submitting a patch.
>>
>> Users don't want to convert gigabytes of .mrc files to tiff before
>> they put them in OMERO
>> and lose all the meta data in the process!
>>
>> Maybe its a more general question....
>> does OMERO.import aim to work for all data file types that bio- 
>> formats
>> can read, or just a subset of those?
>>
>> cheers
>>
>> Dan
>>
>>
>>
>> On Jul 10, 2009, at 11:57 AM, Björn Quast wrote:
>>
>>> Hi Dan,
>>>
>>> I guess you mean .mrc files from imod (http://bio3d.colorado.edu/
>>> imod/). Perhaps you can save them as one multilayer tif-file with
>>> imagej or export the layers as single tif-files by using the command
>>> line, mrc2tif <mrc-file> <basename_for_tif-files>.
>>>
>>> You can reconvert the tifs to mrc with tif2mrc. But I am not sure if
>>> this all helps you, if you want to keep your metadata with the mrc-
>>> files.
>>>
>>> cheers
>>>
>>> Björn
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> Am Freitag, 10. Juli 2009 11:26:20 schrieb Daniel James White:
>>>> Hi All,
>>>>
>>>> I see bio-formats reads .mrc files from electron microscopy,
>>>> but OMERO.import doesnt seem to like them?
>>>> They are not in the list of acceptable file types.
>>>>
>>>> Can i add .mrc somehow?
>>>>
>>>>
>>>> cheers
>>>>
>>>> Dan
>>>>
>>>> Dr. Daniel James White BSc. (Hons.) PhD
>>>> Senior Microscopist / Image Visualisation, Processing and Analysis
>>>> Light Microscopy and Image Processing Facilities
>>>> Max Planck Institute of Molecular Cell Biology and Genetics
>>>> Pfotenhauerstrasse 108
>>>> 01307 DRESDEN
>>>> Germany
>>>>
>>>> +49 (0)15114966933 (German Mobile)
>>>> +49 (0)351 210 2627 (Work phone at MPI-CBG)
>>>> +49 (0)351 210 1078 (Fax MPI-CBG LMF)
>>>>
>>>> http://www.bioimagexd.net BioImageXD
>>>> http://pacific.mpi-cbg.de Fiji Fiji is just ImageJ - Batteries
>>> Included
>>>> http://www.chalkie.org.uk
>>>> dan at chalkie.org.uk
>>>> ( white at mpi-cbg.de )
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> ome-users mailing list
>>>> ome-users at lists.openmicroscopy.org.uk
>>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>>
>>>
>>> -- 
>>> Dr. Björn Quast
>>> Universität Bonn
>>> Institut für Evolutionsbiologie und Ökologie
>>> 53121 Bonn
>>> Tel.: 0228/735758 email: bquast at evolution.uni-bonn.de
>>>
>>
>> Dr. Daniel James White BSc. (Hons.) PhD
>> Senior Microscopist / Image Visualisation, Processing and Analysis
>> Light Microscopy and Image Processing Facilities
>> Max Planck Institute of Molecular Cell Biology and Genetics
>> Pfotenhauerstrasse 108
>> 01307 DRESDEN
>> Germany
>>
>> +49 (0)15114966933 (German Mobile)
>> +49  (0)351 210 2627 (Work phone at MPI-CBG)
>> +49  (0)351 210 1078 (Fax MPI-CBG LMF)
>>
>> http://www.bioimagexd.net 	BioImageXD
>> http://pacific.mpi-cbg.de Fiji 	Fiji is just ImageJ - Batteries  
>> Included
>> http://www.chalkie.org.uk
>> dan at chalkie.org.uk
>> ( white at mpi-cbg.de )
>>
>>
>>
>>
>>
>>
>>
>>
>> _______________________________________________
>> ome-users mailing list
>> ome-users at lists.openmicroscopy.org.uk
>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
> Brian Loranger
> Software Developer, Open Microscopy Environment
> Division of Gene Regulation and Expression
> University of Dundee
> (The University of Dundee is a registered Scottish charity, No:  
> SC015096)
>

Dr. Daniel James White BSc. (Hons.) PhD
Senior Microscopist / Image Visualisation, Processing and Analysis
Light Microscopy and Image Processing Facilities
Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstrasse 108
01307 DRESDEN
Germany

+49 (0)15114966933 (German Mobile)
+49  (0)351 210 2627 (Work phone at MPI-CBG)
+49  (0)351 210 1078 (Fax MPI-CBG LMF)

http://www.bioimagexd.net 	BioImageXD
http://pacific.mpi-cbg.de Fiji 	Fiji is just ImageJ - Batteries Included
http://www.chalkie.org.uk
dan at chalkie.org.uk
( white at mpi-cbg.de )