Exception thrown when importing Micro Manager 2.0 dataset with Bioformats

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Exception thrown when importing Micro Manager 2.0 dataset with Bioformats

David Barry

Hi All,

 

I’m having an issue importing some Micro manager datasets with Bio Formats. If I select Plugins > Bio-formats > Bio-formats importer and select an OME TIFF file, the image opens without any issue. However, if I direct bioformats to the metadata.txt file (which, as I understand it, is the recommended approach), the following exception is thrown:

 

(Fiji Is Just) ImageJ 2.0.0-rc-65/1.52b; Java 1.8.0_151 [64-bit]; Windows 10 10.0; 441MB of 98162MB (<1%)

 

java.lang.NumberFormatException: For input string: ""

at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)

at java.lang.Integer.parseInt(Integer.java:592)

at java.lang.Integer.parseInt(Integer.java:615)

at loci.formats.in.MicromanagerReader.parsePosition(MicromanagerReader.java:757)

at loci.formats.in.MicromanagerReader.parsePosition(MicromanagerReader.java:433)

at loci.formats.in.MicromanagerReader.initFile(MicromanagerReader.java:297)

at loci.formats.FormatReader.setId(FormatReader.java:1397)

at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:499)

at loci.plugins.in.ImportProcess.execute(ImportProcess.java:142)

at loci.plugins.in.Importer.showDialogs(Importer.java:140)

at loci.plugins.in.Importer.run(Importer.java:76)

at loci.plugins.LociImporter.run(LociImporter.java:78)

at ij.IJ.runUserPlugIn(IJ.java:222)

at ij.IJ.runPlugIn(IJ.java:186)

at ij.Executer.runCommand(Executer.java:137)

at ij.Executer.run(Executer.java:66)

at java.lang.Thread.run(Thread.java:748)

 

Some of my colleagues have reported seeing this exception regardless of whether they point bioformats to the OME TIFF file or the metadata file. Through a little investigation, I have found that the problem seems to be related to the “UserData” property in the metadata file - deleting this resolves the problem, which leads me to believe that it is not correctly formatted:

 

“UserData”: {

“IJType”: {

“PropVal”: “1”,

“PropType”: “String”

},

“GridRow”: {

“PropVal”: “0”,

“PropType”: “String”

},

“Comment”: {

“PropVal”: “”,

“PropType”: “String”

},

“UUID”: {

“PropVal”: “b8ff797d-4ca2-4770-bf46-17057f11bad7”,

“PropType”: “String”

},

“Height”: {

“PropVal”: “2048”,

“PropType”: “String”

},

“GridColumn”: {

“PropVal”: “0”,

“PropType”: “String”

},

“CameraTimeout”: {

“PropVal”: “20000”,

“PropType”: “String”

},

“Depth”: {

“PropVal”: “2”,

“PropType”: “String”

},

“BitDepth”: {

“PropVal”: “16”,

“PropType”: “String”

},

“KeepShutterOpenChannels”: {

“PropVal”: “false”,

“PropType”: “String”

},

“PixelType”: {

“PropVal”: “GRAY16”,

“PropType”: “String”

},

“Source”: {

“PropVal”: “Micro-Manager”,

“PropType”: “String”

},

“TimeFirst”: {

“PropVal”: “false”,

“PropType”: “String”

},

“ChColors”: {

“PropVal”: “[-1,-13382401,-65536,-16711834]”,

“PropType”: “String”

},

“SlicesFirst”: {

“PropVal”: “false”,

“PropType”: “String”

},

“Width”: {

“PropVal”: “2048”,

“PropType”: “String”

},

“Positions”: {

“PropVal”: “27”,

“PropType”: “String”

},

“ROI”: {

“PropVal”: “[0,0,2048,2048]”,

“PropType”: “String”

}

}

 

If anyone could shed any light on why micro manager appears to be generating incorrectly formatted metadata files, it would be much appreciated. I have noticed that the bioformats JARS micro manager uses are somewhat outdated (formats-common-5.1.1.jar, for example), but replacing them with more recent versions seems to cause issues.

 

Thanks,

 

Dave.

 

 

Dave Barry,

Image Analyst,

Crick Advanced Light Microscopy Facility (CALM),

The Francis Crick Institute,

1 Midland Road,

London,

NW1 1AT.

 

T: +44 20379 60913

E: [hidden email]

W: www.crick.ac.uk

R: SW312

 

The Francis Crick Institute Limited is a registered charity in England and Wales no. 1140062 and a company registered in England and Wales no. 06885462, with its registered office at 1 Midland Road London NW1 1AT


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