[ome-users] small issue with recent MetaXpress XML formatting

[Sebastien Besson (Staff)]

Hi Mario,

as always thanks for the email and the link to your sample file.
Which version of Bio-Formats are you using? With the version 5.1.4 of
Bio-Formats, the separator you are mentioning is indeed converted to
“ #13 #10” and should be properly handled in the parseXML step [1] [2].

So the list of values stored in the first Description property is correctly
parsed into metadata key/value pairs when calling showing on your
sample file:

 $ showinf -nopix bxyz-505_wA03_s1_z1_t1_cDAPI_u1.tif
Checking file format [Metamorph TIFF]
Initializing reader
MetamorphTiffReader initializing bxyz-505_wA03_s1_z1_t1_cDAPI_u1.tif
...
Reading global metadata
ApplicationName: MetaMorph
ApplicationVersion: 5.1.0.46
Binning: 1 x 1
BitsPerSample: 16
Camera Bit Depth: 14
Camera Shutter: Always Open
Clear Count: 2
Clear Mode: CLEAR PRE SEQUENCE
Compression: Uncompressed
DateTime: 20150828 10:17:04.11
Digitizer: 10 MHz
Exposure: 10 ms
Frames to Average: 1
Gain: Gain 1 (0.5x)
ImageLength: 1040
ImageWidth: 1392
ImageXpress Micro Filter Cube: DAPI
ImageXpress Micro Objective: 10x Plan Fluor
ImageXpress Micro Shutter: Open
Lumencor Blue Intensity: 255
Lumencor Blue Shutter: Closed
Lumencor Cyan Intensity: 255
Lumencor Cyan Shutter: Closed
Lumencor Green Intensity: 255
Lumencor Green Shutter: Closed
Lumencor Red Intensity: 255
Lumencor Red Shutter: Closed
Lumencor Teal Intensity: 255
Lumencor Teal Shutter: Closed
Lumencor UV Intensity: 255
Lumencor UV Shutter: Closed
MetaDataPhotometricInterpretation: Monochrome
MetaDataVersion: 1
NewSubfileType: 2
NumberOfChannels: 1
Orientation: 1st row - top; 1st column - left
PhotometricInterpretation: BlackIsZero
Region: 1392 x 1040, offset at (0, 0)
SamplesPerPixel: 1
Shading: Off
Software: MetaSeries
Subtract: Off
Temperature: -29.75
Trigger Mode: Normal (TIMED)
…


Best,
Sebastien

[1] https://github.com/openmicroscopy/bioformats/blob/v5.1.4/components/formats-gpl/src/loci/formats/in/MetamorphTiffReader.java#L244
[2] https://github.com/openmicroscopy/bioformats/blob/v5.1.4/components/formats-gpl/src/loci/formats/in/MetamorphHandler.java#L128

On 4 Sep 2015, at 12:52, Mario Emmenlauer <mario at emmenlauer.de<mailto:mario at emmenlauer.de>> wrote:


Dear Bio-Formats developers,

I have a small issue with MetaXpress meta data. I could already track
down a bit of detail: The MetaXpress meta data can contain an XML
string, that will be read in loci/formats/in/MetamorphTiffReader.java.
The XML can contain a value="..." that is itself a list again, which
in earlier versions of MetaXpress was separated by "&#13;&#10;"
In newer versions of MetaXpress there seems to be a change, that the
list is instead separated by "
" (note the different ampersand).

Now the problem comes around line 244 of MetamorphTiffReader.java, where
there is a call to XMLTools.sanitizeXML(ifd.getComment()); After the
sanitizing, the ampersand is gone, leaving " #13; #10;" behind, which
is a problem for my subsequent parsers. Would it be possible to change
the behavior of sanitizeXML() to leave intact the list separator? Or
maybe you have another better solution...

The image I used is here:
   http://data.marssoft.de/bxyz-505_wA03_s1_z1_t1_cDAPI_u1.tif

All the best, and thanks for your great work,

    Mario Emmenlauer






--
Mario Emmenlauer BioDataAnalysis             Mobil: +49-(0)151-68108489
Balanstrasse 43                    mailto: mario.emmenlauer * unibas.ch<http://unibas.ch>
D-81669 München                          http://www.marioemmenlauer.de/


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