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

[Melissa Linkert]

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.

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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