[ome-users] Bug in Bio-Formats/Fiji

[David Gault (Staff)]

Hi Jacob,

Thank you for providing those extra details. I have opened a Bio-Formats PR to test and review a potential fix for this issue which you can follow at the link below:
https://github.com/openmicroscopy/bioformats/pull/2981

With Thanks,
David Gault

On 17 Oct 2017, at 16:32, Jacob Seifert <derduxon at gmail.com<mailto:derduxon at gmail.com>> wrote:

Hi David,

thanks for your reply. The sample file comes from 'Fluorescence Lifetime Imaging (FLIM)', therefore containing photon counts per time channel and pixel. Many (almost all) of them contain zero counts. Can this contribute to the smaller than expected data block size?

Importing the sample file with the proprietary SPCImage software provides the following information.

-- Measurement Info --
Size-X: 256
Size-Y: 256
Time channels: 1024
Routing channels: 1
Time Range [ns]: 16.68
Count Increment: 1
Columns: 1


This is all I know so far. If I can provide more useful information, please let me know.

Regards,
Jacob



On Tue, Oct 17, 2017 at 5:00 PM David Gault (Staff) <d.gault at dundee.ac.uk<mailto:d.gault at dundee.ac.uk>> wrote:
Hi Jacob,

I was able to test and reproduce the issue as reported with the sample file provided.The problem appears to be that the expected data block size is much larger than the available space.

The metadata appears to be read correctly and matches with the details provide, however for an expected 256*256 pixels with 1024 channels the file size does seem much smaller than would be required.
Would you be able to provide further details as to the type of image data expected within the datablock?

With Thanks,
David Gault

> On 16 Oct 2017, at 12:20, Jacob Seifert <derduxon at gmail.com<mailto:derduxon at gmail.com>> wrote:
>
> Dear OME users,
>
> I've encountered a bug while importing *.sdt (Becker & Hickl SPCImage v6.2) files:
>
> (Fiji Is Just) ImageJ 2.0.0-rc-61/1.51n; Java 1.8.0_66 [64-bit]; Windows 7 6.1; 452MB of 6045MB (7%)
>
> java.lang.IllegalArgumentException
> at java.nio.Buffer.position(Buffer.java:244)
> at loci.common.NIOFileHandle.buffer(NIOFileHandle.java:605)
> at loci.common.NIOFileHandle.skipBytes(NIOFileHandle.java:451)
> at loci.common.RandomAccessInputStream.skipBytes(RandomAccessInputStream.java:597)
> at loci.formats.in.SDTInfo.<init>(SDTInfo.java:956)
> at loci.formats.in.SDTReader.initFile(SDTReader.java:393)
> at loci.formats.FormatReader.setId(FormatReader.java:1397)
> at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:498)
> at loci.plugins.in.ImportProcess.execute(ImportProcess.java:141)
> 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:217)
> at ij.IJ.runPlugIn(IJ.java:181)
> at ij.Executer.runCommand(Executer.java:137)
> at ij.Executer.run(Executer.java:66)
> at java.lang.Thread.run(Thread.java:745)
>
>
> Bio-Formats is on version 5.7.1. A non-working file [722 kiB] is attached.
> Metadata of this file: 256x256 pixel image with fluorescence lifetime information in 1024 channels.
>
> Regards,
> Jacob
>
>
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