[ome-users] strange (bad?) meta data with bfopen for MetaXpress
Mario Emmenlauer
mario at emmenlauer.de
Wed Apr 15 08:53:54 BST 2015
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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