[ome-users] strange (bad?) meta data with bfopen for MetaXpress

Fri Jan 23 08:56:22 GMT 2015

Hello,
i receive a lot of email from you .
please be sure that you send them at the correspond contact.
thank you

2015-01-22 15:44 GMT+01:00 Mario Emmenlauer <mario at emmenlauer.de>:

>
> Hi Melissa,
>
> On 21.01.2015 23:31, Melissa Linkert wrote:
> > Hi Mario,
> >
> >> attached is an image from MetaXpress, where I try to read all
> >> available meta data. However there are some values that seem not
> >> to make sense, can you please help if there is a bug, or if the
> >> values are indeed correct, or possibly if the issue is in Meta-
> >> Xpress that stores weired values? Examples are:
> >>     Channel #0 Laser focus score    8.2890462076516E-310
> >>     Channel #0 Camera Bit Depth     8.289046E-317
> >
> > Thank you for the bug report - this is indeed a bug in Bio-Formats.  We
> > have a fix under review now:
> >
> > http://github.com/openmicroscopy/bioformats/pull/1537
> >
> > I would expect that to be included in the upcoming 5.0.7 and 5.1.0
> > releases.
>
> Thanks for the very quick fix, its appreciated! I'll wait for the
> 5.0.7 or 5.1.0 releases to check the result.
>
> All the best,
>
>     Mario
>
>
>
> > Regards,
> > -Melissa
> >
> > On Wed, Jan 21, 2015 at 08:52:41PM +0100, Mario Emmenlauer wrote:
> >>
> >> Dear Bio-Formats developers,
> >>
> >> attached is an image from MetaXpress, where I try to read all
> >> available meta data. However there are some values that seem not
> >> to make sense, can you please help if there is a bug, or if the
> >> values are indeed correct, or possibly if the issue is in Meta-
> >> Xpress that stores weired values? Examples are:
> >>     Channel #0 Laser focus score    8.2890462076516E-310
> >>     Channel #0 Camera Bit Depth     8.289046E-317
> >>
> >> These (and some others) seem not to make sense(?) Attached is
> >> also the meta data that I can extract with Bio-Formats from the
> >> latest Fiji, I believe version Bio-Formats 5.0.6.
> >>
> >> All the best,
> >>
> >>      Mario
> >>
> >>
> >>
> >>
> >>
> >> --
> >> Mario Emmenlauer BioDataAnalysis             Mobil: +49-(0)151-68108489
> >> Balanstrasse 43                    mailto: mario.emmenlauer * unibas.ch
> >> D-81669 München                          http://www.marioemmenlauer.de/
> >
> >
> >> Key  Value
> >>  BitsPerPixel        16
> >>  DimensionOrder      XYCZT
> >>  IsInterleaved       false
> >>  IsRGB       false
> >>  LittleEndian        true
> >>  PixelType   uint16
> >>  Series 0 Name
> >>  SizeC       1
> >>  SizeT       1
> >>  SizeX       1392
> >>  SizeY       1040
> >>  SizeZ       1
> >> AbsoluteZ    2096309
> >> AbsoluteZValid       0
> >> AutoScale    1
> >> AutoScaleHiInfo      0/1
> >> AutoScaleLoInfo      0/1
> >> Binning      1 x 1
> >> BitsPerSample        16
> >> CalibrationUnits     ume
> >> Camera Shutter       Always Open
> >> CameraBin    1x1
> >> CameraChipOffset     2096260
> >> Channel #0 Camera Bit Depth  8.289046E-317
> >> Channel #0 ImageXpress Micro Filter Cube     Cy5
> >> Channel #0 ImageXpress Micro Objective       10X S Fluor
> >> Channel #0 ImageXpress Micro Shutter Open
> >> Channel #0 Laser focus score 8.2890462076516E-310
> >> Channel #0 Lumencor Blue Intensity   8.289046E-317
> >> Channel #0 Lumencor Blue Shutter     Closed
> >> Channel #0 Lumencor Cyan Intensity   8.289046E-317
> >> Channel #0 Lumencor Cyan Shutter     Closed
> >> Channel #0 Lumencor Green/Yellow Intensity   8.289046E-317
> >> Channel #0 Lumencor Green/Yellow Shutter     Closed
> >> Channel #0 Lumencor Red Intensity    8.289046E-317
> >> Channel #0 Lumencor Red Shutter      Closed
> >> Channel #0 Lumencor Teal Intensity   8.289046E-317
> >> Channel #0 Lumencor Teal Shutter     Closed
> >> Channel #0 Lumencor UV Intensity     8.289046E-317
> >> Channel #0 Lumencor UV Shutter       Closed
> >> Channel #0 _IllumSetting_    Cy5
> >> Channel #0 _MagNA_   8.28904606E-316
> >> Channel #0 _MagRI_   8.289046E-317
> >> Channel #0 _MagSetting_      10X S Fluor
> >> Clear Count  2
> >> Clear Mode   CLEAR PRE SEQUENCE
> >> Compression  LZW
> >> DateTime     19/03/2014 12:59:47:667
> >> Digitizer    20 MHz
> >> Exposure     100 ms
> >> FillOrder    Pixels with lower column values are stored in the higher
> order bits of a byte
> >> Frames to Average    1
> >> Gain Gain 1 (1x)
> >> Gamma        2096317
> >> ImageLength  1040
> >> ImageWidth   1392
> >> LastSavedTime        19/03/2014 12:59:47:790
> >> Location     /tmp/b0BCDSL-T070_wD07_s4_z0_t1_cCy5_u001.tif
> >> MaxScale     4095
> >> MetaDataPhotometricInterpretation    Monochrome
> >> MinScale     194
> >> Name Cy5
> >> NewLUT       8
> >> NewSubfileType       0
> >> NumberOfChannels     1
> >> PhotometricInterpretation    BlackIsZero
> >> PlanarConfiguration  Chunky
> >> PlaneProperty        2097094
> >> Predictor    Horizontal differencing
> >> Region       1392 x 1040, offset at (0, 0)
> >> ResolutionUnit       Inch
> >> SamplesPerPixel      1
> >> Shading      Off
> >> Software     MetaMorph 3.1.0.79
> >> Spatial Calibration  on
> >> StagePosition        2096244
> >> StandardLUT  monochrome
> >> Subtract     Off
> >> Temperature  -29.85
> >> ThreshState  off
> >> ThreshStateBlue      64
> >> ThreshStateGreen     128
> >> ThreshStateHi        65535
> >> ThreshStateLo        0
> >> ThreshStateRed       255
> >> Trigger Mode Normal (TIMED)
> >> Wavelength   692
> >> XCalibration 645/1000
> >> XResolution  72
> >> YCalibration 645/1000
> >> YResolution  72
> >> Zoom 35
> >> grayFit      4
> >> grayMax      -1/1
> >> grayMin      -1/1
> >> grayPointCount       0
> >> grayX        -1/1
> >> grayY        -1/1
> >
> >> _______________________________________________
> >> ome-users mailing list
> >> ome-users at lists.openmicroscopy.org.uk
> >> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
> >
> >
>
> --
> A: Yes.
> > Q: Are you sure?
> >> A: Because it reverses the logical flow of conversation.
> >>> Q: Why is top posting annoying in email?
>
> Mario Emmenlauer BioDataAnalysis             Mobil: +49-(0)151-68108489
> Balanstrasse 43                    mailto: mario.emmenlauer * unibas.ch
> D-81669 München                          http://www.biodataanalysis.de/
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
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