[ome-users] .mrc file import into omero
Daniel James White
white at mpi-cbg.de
Fri Jul 10 13:11:27 BST 2009
Hi Will (and Quentin)
On Jul 10, 2009, at 1:29 PM, Will Moore wrote:
> Hi Dan,
>
> I just tried opening a sample .mrc file with the BioFormats
> importer in imageJ.
>
> Although there is a small amount of "original metadata" displayed
> (see below), there is no metadata in the ome-xml, other than the XYZ
> pixel dimensions.
well at least thats something!
>
> I have no idea how much other metadata is associated with this .mrc
> file or with a "typical" .mrc file or whether BioFormats is missing
> something here?
me neither really... i haven't looked at the .mrc file format spec yet
to see what can be in there...
>
> However, the reason that the ome-xml is so poorly populated with
> metadata is that EM metadata does not map onto our data model.
Right, i see the issue.
>
> This fact will also cause problems when you try to import .mrc files
> into OMERO and look for somewhere to put the metadata.
> Your options will be to either create some structured annotations
> for the various pieces of metadata, or to attach a text file with
> the metadata to images.
> These approaches may work on a small scale, but would not scale well
> to large numbers of images.
but at least OMERO could still act as a database for archiving and
organising the images,
and browsing them remotely, along with the ability to add
dcoumentation with omero.editor and tag datasets with keywords etc.
its nice to have ALL the meta data available, but with at least xyz
dimensions the data can be at least viewed with a scale bar.
>
> A more complete solution would involve altering the database to
> model the EM metadata.
right
>
> As has been mentioned, we are planning to support EM images in OMERO
> in a project spanning the next 3 years, in a collaboration with the
> EM DB at EBI.
> This includes building a complete data model for EM data (as we have
> done for light microscopy) and implementing this in BioFormats, the
> OMERO server and clients.
>
> As the OMERO team has little experience of EM to date, any help that
> you can provide in this area would be most welcome!
Quentin is the guy here wgho is involved and interested in image
database solutions for electron microscopy,
and i wonder if he might like to help you define the EM meta data model.
He has a much better i dea than i do about that meta data is really
important for EM.
cheers
Dan
>
>
> DimensionOrder XYZTC
> IsInterleaved true
> IsRGB false
> LittleEndian false
> PixelType uint8
> SizeC 1
> SizeT 1
> SizeX 256
> SizeY 256
> SizeZ 32
> Alpha angle 256.0
> Angle 1 0.0
> Angle 2 0.0
> Angle 3 0.0
> Angle 4 0.0
> Angle 5 0.0
> Angle 6 0.0
> Beta angle 256.0
> Gamma angle 32.0
> Label 1 CIDS: Digitized with Photometrics STAR1 CCD 21-
> APR-93
> Label 2 16:11:40 NEWSTACK: Images copied,
> transformed 22-APR-93 1
> Label 3 0:37:25 NEWSTACK: Images copied,
> transformed 28-APR-93 1
> Label 4 1:16:27 FIXMONT: 120 sections
> replaced 28-APR-93 1
> Label 5 3:11:58 MRCFLOAT: Float to common
> mean 28-APR-93 15:09:1
> Label 6 7 1 degree tilt reconstruction, parallel to tilt
> axis 28-APR-
> Label 7 93 17:31:52mrcbyte: Converted and scaled to byte mode.
> Mon Aug 15 12:59:51
> Label 8 1994
> mrcbyte: Converted and scaled to byte mode. Mon Aug 15
> 14:28:03
> Label 9 1994
>
> Lens 0
> Local machine /Volumes/ome/data_repo/from_skyking/mrc/samples/
> golgi.mrc
> Maximum pixel value 2.8E-45
> Mean pixel value 4.2E-45
> Minimum pixel value 1.4E-45
> ND1 0
> ND2 0
> Number of useful labels 0
> Pixel size (X) Infinity
> Pixel size (Y) Infinity
> Pixel size (Z) Infinity
> Series type mono
> VD1 0
> VD2 0
>
>
> On 10 Jul 2009, at 11:52, Daniel James White wrote:
>
>> 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 )
>>
>>
>>
>>
>>
>>
>>
>>
>> _______________________________________________
>> ome-users mailing list
>> ome-users at lists.openmicroscopy.org.uk
>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
> William Moore
> Division of Gene Regulation and Expression
> College of Life Sciences
> University of Dundee
> Scotland
> DD1 5PH
>
> Tel 01382 386364
>
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 )
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