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

Fernandez, Pablo pablo.fernandez at tum.de
Fri Apr 20 07:32:54 BST 2018 

Hi David,


thank you very much for your quick help.


The problem seems to arise when we abort the acquisition.

µManager failed to cleanup files due to some issue

with the camera shutter, thus the last frame in the

metadata text file stops at the shutter line.


I haven't managed to correct the metadata properly so that

matlab can load the data, but I found a much simpler solution: just remove the metadata file.


Cheers,

pablo



________________________________
Von: ome-users <ome-users-bounces at lists.openmicroscopy.org.uk> im Auftrag von David Gault (Staff) <d.gault at dundee.ac.uk>
Gesendet: Donnerstag, 19. April 2018 14:11:00
An: OME User Support List
Betreff: Re: [ome-users] problem loading multiple ome.tiff files in Matlab

Hi Pablo,

I was able to test the uploaded file you submitted and reproduced the second issue you were seeing, NoSuchElementException.

From looking at the metadata text file it appears that the the last FrameKey at the end of the file is missing its losing bracket “}”, adding this back into the file should resolve the NoSuchElementException and allow the file to be read. It does look as though that last frame also has less metadata than previous entries so it may be worth checking that the data at the end of the file is correct and all present.

Also as a side note there is a bug fix for the MicroManagerReader included in the upcoming Bio-Formats 5.8.2 release which may help with some of these issues.

With Thanks,
David Gault

On 18 Apr 2018, at 15:29, Fernandez, Pablo <pablo.fernandez at tum.de<mailto:pablo.fernandez at tum.de>> wrote:

Hi David,

I just uploaded it. Thank you very much
for looking at this.

Incidentally, depending on the particular set of files
I sometimes get a different error message, namely:


Error using bfGetReader (line 85)
Java exception occurred:
java.util.NoSuchElementException

    at java.util.StringTokenizer.nextToken(Unknown Source)

    at loci.formats.in.MicromanagerReader.parsePosition(MicromanagerReader.java:870)

    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)


________________________________
Von: ome-users <ome-users-bounces at lists.openmicroscopy.org.uk<mailto:ome-users-bounces at lists.openmicroscopy.org.uk>> im Auftrag von David Gault (Staff) <d.gault at dundee.ac.uk<mailto:d.gault at dundee.ac.uk>>
Gesendet: Mittwoch, 18. April 2018 11:36:25
An: OME User Support List
Betreff: Re: [ome-users] problem loading multiple ome.tiff files in Matlab

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


-------------------------------------------
Tel +49-(0)89-289-12490
E27 Zellbiophysik
Technische Universität München
James-Franck-Straße 1
D 85748 Garching b. München


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