[ome-users] strange (bad?) meta data with bfopen for MetaXpress
Melissa Linkert
melissa at glencoesoftware.com
Wed Apr 15 17:57:31 BST 2015
Hi Mario,
> I've seen progress reported in your issue tracker for this!
> But I could not easily understand if its in a state that would
> make sense for me to try? Even if incomplete, I might be able
> to aid development by testing the current snapshot on our ~5k
> image sets?
>
> If you think it makes sense, can you point out how I fetch the
> patch and integrate it in my local GIT? From there on I know my
> way...
This ticket:
> >> http://trac.openmicroscopy.org/ome/ticket/12802
currently does not have a proposed fix - we've investigated enough to
know that we won't have time to fix it for the upcoming 5.1.1, but we
expect to have a fix for 5.1.2. Apologies for any confusion there.
When we have a proposed fix, we will update the ticket with a link to
the pull request on GitHub. At that point, you can build the patch by
adding the correct remote (SOMEUSER will be the username shown in the
pull request):
http://www.openmicroscopy.org/site/support/contributing/using-git.html#github-remotes
fetch the remote as shown on that page, and then merge the branch name
given in the pull request. We can certainly provide more detailed
commands once a pull request is open and the remote name/branch name is
known.
Regards,
-Melissa
On Wed, Apr 15, 2015 at 09:53:54AM +0200, Mario Emmenlauer wrote:
>
> Dear Melissa and all,
>
> I've seen progress reported in your issue tracker for this!
> But I could not easily understand if its in a state that would
> make sense for me to try? Even if incomplete, I might be able
> to aid development by testing the current snapshot on our ~5k
> image sets?
>
> If you think it makes sense, can you point out how I fetch the
> patch and integrate it in my local GIT? From there on I know my
> way...
>
> Thanks for your help, and Cheers,
>
> Mario
>
>
>
> On 26.03.2015 14:34, Mario Emmenlauer wrote:
> >
> > Dear Melissa,
> >
> > On 25.03.2015 23:13, Melissa Linkert wrote:
> >>> 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
> >
> > Thanks for the very fast follow-up! I'll follow the ticket!
> >
> > Cheers,
> >
> > Mario
> >
> >
> >
> >
> >> 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
> >>
> >
>
> --
> 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/
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