[ome-users] Bug-report Leica timestamps

[Sebastien Besson (Staff)]

Hi Marjolein,

thanks for uploading the file and some minimal code. Unfortunately, I was
not able to reproduce either with MATLAB or Fiji and Bio-Formats 5.5.3, e.g.

>> [~,v]=bfCheckJavaPath

v =

5.5.3

>> Reader = bfGetReader('BugReport_MM.lif');
Reader.setSeries(0);
omeMeta = Reader.getMetadataStore();
deltaT = omeMeta.getPlaneDeltaT(0,0)

deltaT =

ome.units.quantity.Time: value[0.0], unit[s] stored as java.lang.Double

>> deltaT2 = omeMeta.getPlaneDeltaT(0,1)

deltaT2 =

ome.units.quantity.Time: value[16.53299903869629], unit[s] stored as java.lang.Double

Support for recent LIF timestamps has been added in Bio-Format 5.3.3 [1]. Can you confirm
the version and the revision of Bio-Formats used (as given by
loci.formats.FormatTools.VCS_REVISION in MATLAB or the About Plugins > Bio-Formats Plugins…
menu in Fiji)?

Best,
Sebastien

[1] https://github.com/openmicroscopy/bioformats/pull/2728

On 18 Jul 2017, at 22:13, Marjolein Meddens <marjolein at unm.edu<mailto:marjolein at unm.edu>> wrote:

Hello.

I think I found a bug in Bio-Formats.
The issue is that I’m not able to load time stamps from my Leica .lif files. I ran into the problem while using Matlab toolbox, but I checked whether I could get the time stamps in Fiji and I also couldn’t get them there.
One thing to note is that my data was acquired using “Live Data Mode” which allows you to acquire different ‘jobs’ in the Leica software.
I can see the timestamps in the LASX software (see screenshot) so they’re saved in the lif file.

I have uploaded my file on the QA system. (BugReport_MM.lif).

Code that reproduces problem in Matlab:
Reader = bfGetReader('BugReport_MM.lif');
Reader.setSeries(0);
omeMeta = Reader.getMetadataStore();
deltaT = omeMeta.getPlaneDeltaT(0,0); %deltaT is empty

Code that reproduces problem in Fiji
run("Bio-Formats Macro Extensions");
Ext.setId("Y:\\Marjolein\\OME bug report\\BugReport_MM.lif")
Ext.getPlaneTimingDeltaT(deltaT, 1)
print(deltaT); // deltaT is NaN

System info:
Windows 8.1 Enterprise 64-bit
Java 1.8.0_111
BioFormats 5.5.3

Thank you,
Marjolein

Marjolein Meddens PhD | Postdoc

Department of Physics and Astronomy
Department of Pathology
University of New Mexico
Albuquerque, USA


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