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

Wed Mar 25 10:57:04 GMT 2015

Dear Bio-Formats developers,

I've checked the current trunk for below-mentioned fix, and I think
most values are fine now! There is one exception where I'm uncertain
about the value: "Gamma" is returned as "2096317", which to me looks
possibly incorrect (and actually looks more like a TIFF offset than
a value). 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/