Open Microscopy Environment

Hi all,

I'm using the latest version of bioformats (5.1.7) and I receive a strange error message for some of the nd2 files I'm trying to read.

When I'm reading a 96 series of 3 channel images (2765x3629 pixels each image) the function works perfectly.

However, recently I'm receiving the following error messages for the same series but with a bit larger images (3636x4772 pixels each image):
Java exception occurred:
java.lang.IndexOutOfBoundsException: Index: 0, Size: 0

at java.util.ArrayList.rangeCheck(Unknown Source)
at java.util.ArrayList.get(Unknown Source)
at loci.formats.FormatReader.getSizeC(FormatReader.java:719)
at loci.formats.in.NativeND2Reader.initFile(NativeND2Reader.java:1342)
at loci.formats.FormatReader.setId(FormatReader.java:1426)
at loci.formats.DelegateReader.setId(DelegateReader.java:290)
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)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)
at loci.formats.Memoizer.setId(Memoizer.java:678)


This error occurs in the last line of bfGerReader - r.setId(id) command

P.S.
I increased the java heap memory to 700MB and I get this error in windows 10\7 and linux platforms

Any help would be greatly appreciated.

Hi,

sorry to hear you are experiencing issues opening your ND2 files. The stack trace you pasted below indicates an error at the reader level when your file is getting read by Bio-Formats and is likely independent of the system memory. Sadly, none of the sample nd2 file in our data repository exhibit this issue with Bio-Formats 5.1.7.

In order to investigate it more thoroughly, would it be possible for you to send us your file allowing to reproduce the issue? If the file is smaller than 2GB, you should be able to upload it directly to http://qa.openmicroscopy.org.uk/qa/upload/. Otherwise, we can give you the credentials to a FTP server where larger files can be uploaded.

Best,
Sebastien

Hi!

Thanks for the response.
The original file is almost 8GB so I won't be able to upload it through the web.

I cropped the file to several images (300MB) and surprisingly it works and able to read it. As I try to read the whole file it fails once again...

How can I send you guys a 8GB nd2 file?
Thanks!

Hi,

Thank you again for the feedback. I am sending FTP credentials for uploading large files in a private message.

Regards,
-Melissa

I've uploaded it under the name: nd2_updated

many thanks!

Thank you for uploading the problematic file; I can indeed reproduce the problem.

We may not be able to fix the problem in time for the 5.2.0 release, but we should be able to fix it in time for 5.2.1 - see https://trello.com/c/6toIZSzX/1-large-n ... -exception.

Coming back to this thread,

I was unable to duplicate the exception with the uploaded file and Bio-Formats 5.2.0 and above. I suspect this issue was fixed as part of https://github.com/openmicroscopy/bioformats/pull/2284.

Let us know if you still encounter it with the latest version of Bio-Formats.

Best,
Sebastien