[ome-users] strange (bad?) meta data with bfopen for MetaXpress
Melissa Linkert
melissa at glencoesoftware.com
Wed Mar 25 22:13:00 GMT 2015
Hi Mario,
> correcting my own email from 30min ago:
>
> I've checked the current trunk for below-mentioned fix, and I think
> several values are fine now. There are some exceptions where I'm
> uncertain about the value:
> "AbsoluteZ" = "2096309"
> "CameraChipOffset" = "2096260"
> "Gamma" = "2096317"
> "PlaneProperty" = "2097094"
> "StagePosition" = "2096244"
>
> To me, these look possibly incorrect (and actually look more like TIFF
> offsets than values). Is that possible?
That certainly seems likely. As with the PageNumber issue, we won't
have a fix for this in 5.1.0, but a ticket is now open:
http://trac.openmicroscopy.org/ome/ticket/12802
Regards,
-Melissa
On Wed, Mar 25, 2015 at 12:48:12PM +0100, Mario Emmenlauer wrote:
>
> Dear Bio-Formats developers,
>
> correcting my own email from 30min ago:
>
> I've checked the current trunk for below-mentioned fix, and I think
> several values are fine now. There are some exceptions where I'm
> uncertain about the value:
> "AbsoluteZ" = "2096309"
> "CameraChipOffset" = "2096260"
> "Gamma" = "2096317"
> "PlaneProperty" = "2097094"
> "StagePosition" = "2096244"
>
> To me, these look possibly incorrect (and actually look more like TIFF
> offsets than values). Is that possible?
>
> The image I used is the same as before:
> http://data.marssoft.de/b0BCDSL-T070_wD07_s4_z0_t1_cCy5_u001.tif
>
> Cheers,
>
> Mario
>
>
>
> On 22.01.2015 15:44, Mario Emmenlauer wrote:
> >
> > 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
More information about the ome-users
mailing list