[ome-users] strange (bad?) meta data with bfopen for MetaXpress
Mario Emmenlauer
mario at emmenlauer.de
Thu Mar 26 13:34:37 GMT 2015
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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