[ome-users] Stage positions from Zeiss LSM 710, Olympus FluoView 1000, Leica SP/SP5
Will Moore
will at lifesci.dundee.ac.uk
Fri Nov 13 17:28:52 GMT 2009
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
>
> ----------------------------------------------------------------------
>
>
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> ome-users at lists.openmicroscopy.org.uk
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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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