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

[Fernandez, Pablo]

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


-------------------------------------------

Tel +49-(0)89-289-12490

E27 Zellbiophysik

Technische Universität München

James-Franck-Straße 1

D 85748 Garching b. München

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