[ome-users] Stage positions from Zeiss LSM 710, Olympus FluoView 1000, Leica SP/SP5
Jason Swedlow
jason at lifesci.dundee.ac.uk
Sat Nov 14 08:39:30 GMT 2009
Hi Aaron-
Just adding one comment. From our contacts with Carl Zeiss
MicroImaging we've been informally told that there were no changes in
the LSM 710's file formats that we needed to know about. However,
these formats are very complex, and something might have slipped by.
As Will mentioned, the confocal list server might be a good place to
post this (this was the method we used some time ago).
OK, climbing on soapbox:
The current situation-- arbitrary file formats, with essentially any
metadata in any format, and no definitive community notification when
things change-- will only change when customers condition their
purchases on this information being provided. In an ideal world (ok,
a total pipe dream), our OME-XML and Bio-Formats developers would be
notified BEFORE new formats were released and provided specifications
and samples. We're a long way from that, but can get there, with the
community's help. If this community insists that this information
will be provided, we won't be having these problems anymore.
Stepping down. Phew!
Have a great weekend.
Cheers,
Jason
On 13 Nov 2009, at 17:28, Will Moore wrote:
> Hi Aaron,
>
> The key question is whether the stage position metadata is actually
> stored in the file. If it is, then it should be possible for
> BioFormats to identify the correct bit of metadata and store it in
> the OME data model.
>
> We have been working at improving the amount of metadata from these
> confocal formats that is used to populate the OME model. This takes
> time to identify how to read the piece of metadata in the original
> file, and how to map it into the OME model. However, we have so far
> been successful for the various bits of metadata we've attempted so
> far.
>
> There are a couple of ways to determine whether the stage position
> metadata is actually in the file:
> Open the file in the proprietary software (Olympus, Zeiss, Lecia)
> and see if it is displayed.
> Or, open the file in ImageJ, using the BioFormats plugin and look at
> the "Original Metadata".
>
> I've tried these with a sample of the various formats you mentioned,
> and I don't see that any of them have absolute stage positions.
> (some examples below)
> I'm not even sure that BioFormats is reading the Leica stage
> positions properly. Haven't looked at this before.
>
> However, I don't have any LSM 710 files (LSM 510 only), and it's
> also possible that newer versions of these microscopes might save
> this data.
> Some of these files seem to have places in the files for this
> metadata, and it's also possible that the formats might expand to
> accommodate stage metadata.
>
> You could try asking on the confocal lists http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>
> Sorry I couldn't be more help,
>
> Will.
>
>
>
> Looking at the "original metadata" of a couple of oib files, read by
> Bioformats (using the ImageJ plugin). NB. This is all the
> "available" metadata currently read by BioFormats, only a subset of
> this is used to populate the OME data model.
> This is the data available for each plane of the image, shown for
> the first 2 planes of a Z stack.
>
> Image 0 : AS Level 9999
> Image 0 : AbsPositionUnitName mm
> Image 0 : AbsPositionValue 0.0
> Image 0 : Adjust Outward 0
> Image 0 : Adjust Retrun 0
> Image 0 : AnalogPMTGain 1.0
> Image 0 : AnalogPMTOffset 2
> Image 0 : Confocal ON
> Image 0 : CountingPMTGain 0.0
> Image 0 : CountingPMTOffset 1.600000
> Image 0 : CountingPMTVoltage 0
> Image 0 : DataMax 4095.0
> Image 0 : DataMin 0.0
> Image 0 : DataName 1h_after_pdt_C001Z001T001.tif
> Image 0 : DataType WORD
> Image 0 : ExcitationOutPutLevel 5
> Image 0 : HeightConvertValue 0.207
> Image 0 : HeightUnit um
> Image 0 : ImageDepth 2
> Image 0 : ImageGroup Normal
> Image 0 : ImageHeight 1024
> Image 0 : ImageType Intensity
> Image 0 : ImageWidth 1024
> Image 0 : LUTFileName LUT1
> Image 0 : LUTParameter 530227280
> Image 0 : LightControl 9999
> Image 0 : Magnification 60.0
> Image 0 : Name COFAFrameImage
> Image 0 : Number 1
> Image 0 : ObjectiveLens NAValue 1.35
> Image 0 : ObjectiveLens Name UPLSAPO 60X O NA:1.35
> Image 0 : ObjectiveLens WDValue 9999.0
> Image 0 : Observation Mode LSM
> Image 0 : PMTDetectingMode Analog
> Image 0 : PMTVoltage 830
> Image 0 : Pan Scale 2
> Image 0 : Path .\
> Image 0 : PinholeDiameter 115000
> Image 0 : PinholeScale 1
> Image 0 : PixConvertValue 1.0
> Image 0 : PixUnit Intensity
> Image 0 : ROIFileName 530223744_9038484
> Image 0 : Resolution 10.0
> Image 0 : RotationValue 1.0
> Image 0 : RotationValue After Clip 0
> Image 0 : RotationValue Before Clip 10
> Image 0 : SamplingClock 500000
> Image 0 : ScanSpeed 2.0
> Image 0 : Step 0.0
> Image 0 : ValidBitCounts 12
> Image 0 : Version 1.0.0.0
> Image 0 : WidthConvertValue 0.207
> Image 0 : WidthUnit um
> Image 0 : X Pinhole 318
> Image 0 : XPanValue 0
> Image 0 : Y Pinhole -570
> Image 0 : YPanValue 0
> Image 0 : ZoomValue 1.0
>
> Image 1 : AS Level 9999
> Image 1 : AbsPositionUnitName mm
> Image 1 : AbsPositionValue 0.0
> Image 1 : Adjust Outward 0
> Image 1 : Adjust Retrun 0
> Image 1 : AnalogPMTGain 1.0
> Image 1 : AnalogPMTOffset 3
> Image 1 : Confocal ON
> Image 1 : CountingPMTGain 0.0
> Image 1 : CountingPMTOffset 1.600000
> Image 1 : CountingPMTVoltage 0
> Image 1 : DataMax 4095.0
> Image 1 : DataMin 0.0
> Image 1 : DataName 1h_after_pdt_C002Z001T001.tif
> Image 1 : DataType WORD
> Image 1 : ExcitationOutPutLevel 4
> Image 1 : HeightConvertValue 0.207
> Image 1 : HeightUnit um
> Image 1 : ImageDepth 2
> Image 1 : ImageGroup Normal
> Image 1 : ImageHeight 1024
> Image 1 : ImageType Intensity
> Image 1 : ImageWidth 1024
> Image 1 : LUTFileName LUT2
> Image 1 : LUTParameter 530238208
> Image 1 : LightControl 9999
> Image 1 : Magnification 60.0
> Image 1 : Name COFAFrameImage
> Image 1 : Number 1
> Image 1 : ObjectiveLens NAValue 1.35
> Image 1 : ObjectiveLens Name UPLSAPO 60X O NA:1.35
> Image 1 : ObjectiveLens WDValue 9999.0
> Image 1 : Observation Mode LSM
> Image 1 : PMTDetectingMode Analog
> Image 1 : PMTVoltage 700
> Image 1 : Pan Scale 2
> Image 1 : Path .\
> Image 1 : PinholeDiameter 115000
> Image 1 : PinholeScale 1
> Image 1 : PixConvertValue 1.0
> Image 1 : PixUnit Intensity
> Image 1 : ROIFileName 530223744_9038484
> Image 1 : Resolution 10.0
> Image 1 : RotationValue 1.0
> Image 1 : RotationValue After Clip 0
> Image 1 : RotationValue Before Clip 10
> Image 1 : SamplingClock 500000
> Image 1 : ScanSpeed 2.0
> Image 1 : Step 0.0
> Image 1 : ValidBitCounts 12
> Image 1 : Version 1.0.0.0
> Image 1 : WidthConvertValue 0.207
> Image 1 : WidthUnit um
> Image 1 : X Pinhole 318
> Image 1 : XPanValue 0
> Image 1 : Y Pinhole -570
> Image 1 : YPanValue 0
> Image 1 : ZoomValue 1.0
>
> It looks like there might be some parameters for storing stage
> position (e.g. YPanValue) but they are not populated.
> I also don't see any stage position info displayed in the Olympus
> software for this file, so I'm assuming that it is not stored.
> However, I don't have a file format specification to hand, and it's
> also possible that newer microscopes might store this data.
>
>
> Looking at a couple of Leica LIF files, I see that the metadata
> displayed by the software does not include stage position, but if I
> look in the exported metadata, I can see StagePosX="0" StagePosY="0"
> StagePosZ="0". So, the parameters exist in the file but it is not
> written in this case. This may be because the microscope that
> acquired this image was not fitted with a motorized stage?
>
>
>
> On 13 Nov 2009, at 16:05, Ponti, Aaron wrote:
>
>> Hello
>>
>> We are investigating the purchase of one of the following
>> confocals: Zeiss LSM 710, Olympus FluoView 1000, and Leica SP/SP5.
>> One of the criteria for the choice is the possibility to read stage
>> positions from the files (using the loci/ome-xml tools). With
>> loci_tools 4.1 it seems that reading the stage positions into the
>> OME schema is supported for the Leica, but is not for the other
>> two. Can anybody confirm this? Does anybody know if stage positions
>> arestored at all in .lsm and .oib files?
>>
>> Thanks
>>
>>
>> ---------------------------------------------------------------------
>> | Dr. Aaron C. Ponti
>> | Friedrich Miescher Institute for Biomedical Research
>> | Facility for Advanced Microscopy and Imaging
>> | Software development
>> | Maulbeerstrasse 66 CH-4058, Basel
>> | WRO-1066.2.16
>> | Tel: +41 61 696 3513
>> | Fax: +41 61 697 3976
>> | http://www.fmi.ch/faim
>>
>> ----------------------------------------------------------------------
>>
>>
>> _______________________________________________
>> 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
>
> _______________________________________________
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> ome-users at lists.openmicroscopy.org.uk
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