[ome-users] Exception thrown when importing Micro Manager dataset with Bioformats

[David Barry]

Hi David,

Thanks for your response.

We’re using Micro Manager 2.0-beta3. I’ve uploaded a sample metadata file – I can see that the formatting is slightly different and this is obviously the cause of the problem.

Dave.

From: ome-users [mailto:ome-users-bounces at lists.openmicroscopy.org.uk] On Behalf Of David Gault (Staff)
Sent: 23 May 2018 11:48
To: OME User Support List <ome-users at lists.openmicroscopy.org.uk>
Subject: Re: [ome-users] Exception thrown when importing Micro Manager dataset with Bioformats

Hi David,

Do you know which version of Micro Manager you are using? The formatting of the metadata appears to be different from what the reader in Bio-Formats is expecting, you can see examples of the expected metadata format at http://downloads.openmicroscopy.org/images/Micro-Manager/. If you are able to provide a sample file you can submit it to https://www.openmicroscopy.org/qa2/qa/upload/

With Thanks,
David Gault

On 23 May 2018, at 10:30, David Barry <David.Barry at crick.ac.uk<mailto:David.Barry at crick.ac.uk>> wrote:

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: david.barry at crick.ac.uk<mailto:david.barry at crick.ac.uk>
W: www.crick.ac.uk<http://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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