[ome-users] problem loading multiple ome.tiff files in Matlab

[David Gault (Staff)]

Hi Pablo,

Have your files have been saved with a companion metadata file?
If so then uploading it to the link below should provide us with the information required to debug this problem further:
https://www.openmicroscopy.org/qa2/qa/upload/

With Thanks,
David Gault

On 17 Apr 2018, at 15:45, Fernandez, Pablo <pablo.fernandez at tum.de<mailto:pablo.fernandez at tum.de>> wrote:

Hi ome-users,

I am having an issue loading a set of multiple
ome.tiff files in Matlab. The files were created
by micro-manager running a long multidimensional
acquisition, saving the data as a series of 4 GB ome.tiff files,
appending to the filename "_1", "_2" and so on.

Now, I intend to analyze the data in Matlab, so I have
installed bfmatlab.

To my surprise I am able to open all files - except for the first one.
With bfGetReader I get the following error:


Error using bfGetReader (line 85)
Java exception occurred:
java.lang.StringIndexOutOfBoundsException: String index out of range: -2

    at java.lang.String.substring(Unknown Source)

    at loci.formats.in.MicromanagerReader.parsePosition(MicromanagerReader.java:810)

    at loci.formats.in.MicromanagerReader.parsePosition(MicromanagerReader.java:429)

    at loci.formats.in.MicromanagerReader.initFile(MicromanagerReader.java:297)

    at loci.formats.FormatReader.setId(FormatReader.java:1397)

    at loci.formats.ImageReader.setId(ImageReader.java:839)

    at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)

    at loci.formats.ChannelFiller.setId(ChannelFiller.java:223)

    at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)

    at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:291)


I am using Windows 10, Java 8u40, Bioformats 5.8.1.

Incidentally, although the images correspond to stacks at different positions and timepoints µManager stores all frames along the
time direction, as a stack with many timepoints and only one Z
value.

The file is 4 GB large; I will be glad to upload it if that
helps solve the issue.

I would greatly appreciate any help...We are generating
tons of data and really need to analyze it as soon
as possible, before our servers explode 😊

Keep up the great work!
Cheers,
Pablo


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D 85748 Garching b. München


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