[ome-users] strange (bad?) meta data with bfopen for MetaXpress
Mario Emmenlauer
mario at emmenlauer.de
Wed Mar 25 11:48:12 GMT 2015
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/
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