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

[Munro, Ian]

Hi Both

I don’t know if this is relevant  but I note that the file contains the string "SPC FCS Data File”in the header.
Looking at line 92 of https://pimprenelle.lps.ens.fr/xvindoc/SPC__data__file__structure_8h_source.html
this may indicate that the file contains what B&H call FIFO data.

Here there is no image in the file but simply a list of “events” each of which has 2 time tags.
The first tag being a real-time tag and the second being time relative to an  excitation pulse signal taken from a laser..
These events are predominantly the arrival of a detected photon but may also be pixel, line or frame clocks.

 From the clock events and real-time tags it is then possible to generate standard “image” by assigning (binning)each photon to a pixel.

This might explain why the file is smaller than you might expect as this format is much more compact for small numbers of photons.

Best Wishes

Ian



On 18 Oct 2017, at 13:22, David Gault (Staff) <d.gault at dundee.ac.uk<mailto:d.gault at dundee.ac.uk>> wrote:

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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