[ome-users] Stage positions from Zeiss LSM 710, Olympus FluoView 1000, Leica SP/SP5
Ponti, Aaron
aaron.ponti at fmi.ch
Mon Nov 16 09:09:58 GMT 2009
Dear Will and Jason,
Thanks for your feedback. I am posting my question to the confocal lists right away.
Jason, I guess we simply don’t have a community that can make pressure on vendors. I am afraid most buyers do not care much about file formats and the like as long as the optics are good.
a2
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| 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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From: Jason Swedlow [mailto:jason at lifesci.dundee.ac.uk]
Sent: Saturday, November 14, 2009 9:40 AM
To: Ponti, Aaron
Cc: ome-users at lists.openmicroscopy.org.uk OME-Users
Subject: Re: [ome-users] Stage positions from Zeiss LSM 710, Olympus FluoView 1000, Leica SP/SP5
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
----------------------------------------------------------------------
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William Moore
Division of Gene Regulation and Expression
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University of Dundee
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