[ome-users] Imspector msr FLIM

[Balaji Ramalingam (Staff)]

Hi Ewan,

Thank you for submitting your file.
We were able to reproduce the bug locally.

A ticket has been created on this regard,
https://trac.openmicroscopy.org/ome/ticket/13002,
and you have been added to the cc list.

Notifications will be sent to your email id, when there is a status change on the ticket.

Best,
Balaji


__________________

Mr Balaji Ramalingam

Software Developer

OME Team

College of Life Sciences

University of Dundee

From: <Munro>, Ian <i.munro at imperial.ac.uk<mailto:i.munro at imperial.ac.uk>>
Reply-To: OME User Support List <ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>>
Date: Friday, 21 August 2015 14:29
To: OME User Support List <ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>>
Subject: Re: [ome-users] Imspector msr FLIM

Hi Ewan

I can confirm that I am able to reproduce both issues with the current version of FLIMfit.

I have also imported the file which  opens - " 02 - 70 - 1 - tp1 - x16 TCSPC.msr" to the server on demo.openmicroscopy.org<http://demo.openmicroscopy.org>
where the attached ModuloAlong annotation has the same incorrect 1ps time axis.

Running the Bio-Formats showinf command on the other file "01 - 770nm FITC - HybridPMT.msr" gives me the same error

ImspectorReader initializing 01-770nm FITC-HybridPMT.msr
Exception in thread "main" java.lang.ArithmeticException: / by zero
at loci.formats.in.ImspectorReader.initFile(ImspectorReader.java:421)
at loci.formats.FormatReader.setId(FormatReader.java:1426)
at loci.formats.ImageReader.setId(ImageReader.java:835)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)
at loci.formats.tools.ImageInfo.testRead(ImageInfo.java:1013)
at loci.formats.tools.ImageInfo.main(ImageInfo.java:1102)

This suggests that in both cases the issues arise from the Bio-Formats reader rather than FLIMfit or the Matlab interface.
Would it be possible for someone from the Bio-Formats team  to confirm this please?

Regards

Ian




On 21 Aug 2015, at 12:26, Ewan McGhee <e.mcghee at beatson.gla.ac.uk<mailto:e.mcghee at beatson.gla.ac.uk>> wrote:

Hi,

I believe I've encountered a problem trying to use the raw msr files produced by our LaVision Biotec Trim-scopes - specifically, the FLIM data that we acquire.

There seems to be two separate problems:

1. The data taken on the old Trim-scope which runs 32-bit Imspector and uses the LaVisionBiotec x16-TCSPC detector, loads into FLIMFit but the time axis used for measuring the decay is wrong (it shows as 0 to 1 ps, when it should be 0 to 12 ns). The one-tiff export produced by Imspector of the same data, however, loads fine with the correct time axis values.

2. The new Trim-scope we have runs the 64-bit version of Imspector as we have the new hybrid PMT FLIM detectors on this. The msr file produced form this system just crashes out completely -

Error using flim_data_series/get_image_dimensions (line 108)
Java exception occurred:
java.lang.ArithmeticException: / by zero
at loci.formats.in.ImspectorReader.initFile(ImspectorReader.java:421)
at loci.formats.FormatReader.setId(FormatReader.java:1426)
at loci.formats.ImageReader.setId(ImageReader.java:835)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)
at loci.formats.ChannelFiller.setId(ChannelFiller.java:223)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)
at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:289).

I have uploaded an example of each data file to https://www.openmicroscopy.org/qa2/qa/upload/, with the detector type indicated in the file name: 01 - 770nm FITC - HybridPMT.msr and 02 - 70 - 1 - tp1 - x16 TCSPC.msr.

If I can help any other way just let me know.

Cheers,

Ewan
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