[ome-users] Stage positions from Zeiss LSM 710, Olympus FluoView 1000, Leica SP/SP5
Jason Swedlow
jason at lifesci.dundee.ac.uk
Mon Nov 16 09:23:21 GMT 2009
Hi Aaron-
On 16 Nov 2009, at 09:09, Ponti, Aaron wrote:
> 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.
I am much more optimistic-- in the long term. There is alot of
interest from vendors and users-- the customers. If we don't push
this, the problem only gets worse. Optics ARE important. So is
working with your data.
Cheers,
Jason
>
> a2
>
> ---------------------------------------------------------------------
> | 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
>
> ----------------------------------------------------------------------
>
> 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
>
> ----------------------------------------------------------------------
>
>
> _______________________________________________
> 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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>
>
>
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> College of Life Sciences
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> University of Dundee
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> United Kingdom
>
> phone (01382) 385819
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> email: jason at lifesci.dundee.ac.uk
>
> Lab Page: http://gre.lifesci.dundee.ac.uk/staff/jason_swedlow.html
> Open Microscopy Environment: http://openmicroscopy.org
> **************************
>
> The University of Dundee is a Scottish Registered Charity, No.
> SC015096.
>
>
>
**************************
Wellcome Trust Centre for Gene Regulation & Expression
College of Life Sciences
MSI/WTB/JBC Complex
University of Dundee
Dow Street
Dundee DD1 5EH
United Kingdom
phone (01382) 385819
Intl phone: 44 1382 385819
FAX (01382) 388072
email: jason at lifesci.dundee.ac.uk
Lab Page: http://gre.lifesci.dundee.ac.uk/staff/jason_swedlow.html
Open Microscopy Environment: http://openmicroscopy.org
**************************
The University of Dundee is a Scottish Registered Charity, No. SC015096.
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