BioFormats Issues

[Olivier Burri]

Dear All,

As of last week as far as we can tell, we are now having this error with bioformats while opening VSI files

(Fiji Is Just) ImageJ 2.0.0-rc-29/1.49r; Java 1.6.0_24 [64-bit]; Windows NT (unknown) 6.2; 19MB of 18367MB (<1%)
 
java.lang.IllegalArgumentException: Invalid C index: 1/1
        at loci.formats.FormatTools.getIndex(FormatTools.java:410)
        at loci.formats.FormatTools.getIndex(FormatTools.java:337)
        at loci.formats.FormatReader.getIndex(FormatReader.java:1083)
        at loci.formats.in.CellSensReader.initFile(CellSensReader.java:805)
        at loci.formats.FormatReader.setId(FormatReader.java:1395)
        at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:493)
        at loci.plugins.in.ImportProcess.execute(ImportProcess.java:140)
        at loci.plugins.in.Importer.showDialogs(Importer.java:137)
        at loci.plugins.in.Importer.run(Importer.java:75)
        at loci.plugins.LociImporter.run(LociImporter.java:78)
        at ij.IJ.runUserPlugIn(IJ.java:199)
        at ij.IJ.runPlugIn(IJ.java:163)
        at ij.Executer.runCommand(Executer.java:131)
        at ij.Executer.run(Executer.java:64)
        at java.lang.Thread.run(Thread.java:662)


So we contacted Bioformats through their forums and meanwhile tried to revert back to a version that was working. We tried removing all the files relevant to bioformats first by deselecting the update sites LOCI and BioFormats, then by removing anything related to LOCI or bioformats left in the jars and plugins folders, if any.

We then downloaded the previous release of bioformats as a single Jar and tried running it again. The same error. This feels a bit odd, what else should we downgrade to ensure that it is running the same way as before?

Best

Oli

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[ctrueden]

Hi Oli,

> We then downloaded the previous release of bioformats as a single Jar
> and tried running it again. The same error. This feels a bit odd, what
> else should we downgrade to ensure that it is running the same way as
> before?

Did you try downloading and testing with the Nov 2014 Life-Line version of
Fiji, available from the downloads page?

Regards,
Curtis

On Mon, Apr 27, 2015 at 3:15 AM, Burri Olivier <[hidden email]>
wrote:

> Dear All,
>
> As of last week as far as we can tell, we are now having this error with
> bioformats while opening VSI files
>
> (Fiji Is Just) ImageJ 2.0.0-rc-29/1.49r; Java 1.6.0_24 [64-bit]; Windows
> NT (unknown) 6.2; 19MB of 18367MB (<1%)
>
> java.lang.IllegalArgumentException: Invalid C index: 1/1
>         at loci.formats.FormatTools.getIndex(FormatTools.java:410)
>         at loci.formats.FormatTools.getIndex(FormatTools.java:337)
>         at loci.formats.FormatReader.getIndex(FormatReader.java:1083)
>         at loci.formats.in.CellSensReader.initFile(CellSensReader.java:805)
>         at loci.formats.FormatReader.setId(FormatReader.java:1395)
>         at
> loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:493)
>         at loci.plugins.in.ImportProcess.execute(ImportProcess.java:140)
>         at loci.plugins.in.Importer.showDialogs(Importer.java:137)
>         at loci.plugins.in.Importer.run(Importer.java:75)
>         at loci.plugins.LociImporter.run(LociImporter.java:78)
>         at ij.IJ.runUserPlugIn(IJ.java:199)
>         at ij.IJ.runPlugIn(IJ.java:163)
>         at ij.Executer.runCommand(Executer.java:131)
>         at ij.Executer.run(Executer.java:64)
>         at java.lang.Thread.run(Thread.java:662)
>
>
> So we contacted Bioformats through their forums and meanwhile tried to
> revert back to a version that was working. We tried removing all the files
> relevant to bioformats first by deselecting the update sites LOCI and
> BioFormats, then by removing anything related to LOCI or bioformats left in
> the jars and plugins folders, if any.
>
> We then downloaded the previous release of bioformats as a single Jar and
> tried running it again. The same error. This feels a bit odd, what else
> should we downgrade to ensure that it is running the same way as before?
>
> Best
>
> Oli
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[baselta]

Hi Olivier...
I'm a new user to VSI Reader/Bio-Format and I'm facing the same issue.
I uninstalled the latest Fiji and reinstalled the November 2014 release. I then added ActionBar plugin. Then I went to Help>Update Fiji and added auto-update for BIOP, however before accepting changes I "keep as is" all the suggested updates except BIOP. I restarted the software, then went again to Update Fiji and updated Bio-Format. After all this hassle it finally worked. I however don't know if it worked properly or not since this is the first time I used this.

I also found this on Bio-Format website:
"If you get an OutOfMemory or NegativeArraySize error message when attempting to open an SVS or JPEG-2000 file then the amount of pixel data in a single image plane exceeds the amount of memory allocated to the JVM or 2 GB, respectively. For the former, you can increase the amount of memory allocated; in the latter case, you will need to open the image in sections. If you are using Bio-Formats as a library, this means using the openBytes(int, int, int, int, int) method in loci.formats.IFormatReader. If you are using Bio-Formats within ImageJ, you can use the Crop on import option.

Note that JPEG-2000 is a very efficient compression algorithm - thus the size of the file on disk will be substantially smaller than the amount of memory required to store the uncompressed pixel data. It is not uncommon for a JPEG-2000 or SVS file to occupy less than 200 MB on disk, and yet have over 2 GB of uncompressed pixel data."


Thanks.
Basel