[ome-users] strange (bad?) meta data with bfopen for MetaXpress

[Mario Emmenlauer]

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
> 
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>> ome-users at lists.openmicroscopy.org.uk
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> 
> 

-- 
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/