We're Hiring!

Open Microscopy Environment

The OME community

Skip to content

Image J Bioformat SVS or SVI image

Historical discussions about the Bio-Formats library. Please look for and ask new questions at https://forum.image.sc/tags/bio-formats
Please note:
Historical discussions about the Bio-Formats library. Please look for and ask new questions at https://forum.image.sc/tags/bio-formats

If you are having trouble with image files, there is information about reporting bugs in the Bio-Formats documentation. Please send us the data and let us know what version of Bio-Formats you are using. For issues with your code, please provide a link to a public repository, ideally GitHub.
Post a reply

Image J Bioformat SVS or SVI image

Postby benjaminek » Fri Mar 21, 2014 8:54 pm

HEllo,

I am totally new to bioformat.
I have tried to open 2 SVS files (one of around 400 KB, one of 170 KB) this is what happened:
It opens a window with "series 1" though 6 with an image of the svs slide in black and white.


IF i open all series :
ImageJ 1.47v; Java 1.6.0_20 [64-bit]; Windows NT (unknown) 6.2; 29MB of 2986MB (<1%)

java.lang.NegativeArraySizeException
at loci.formats.MinMaxCalculator.openBytes(MinMaxCalculator.java:263)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:305)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:305)
at loci.plugins.util.ImageProcessorReader.openProcessors(ImageProcessorReader.java:190)
at loci.plugins.in.ImagePlusReader.readProcessors(ImagePlusReader.java:416)
at loci.plugins.in.ImagePlusReader.readPlanes(ImagePlusReader.java:380)
at loci.plugins.in.ImagePlusReader.readImage(ImagePlusReader.java:277)
at loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:238)
at loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:216)
at loci.plugins.in.ImagePlusReader.openImagePlus(ImagePlusReader.java:114)
at loci.plugins.in.Importer.readPixels(Importer.java:150)
at loci.plugins.in.Importer.run(Importer.java:89)
at loci.plugins.LociImporter.run(LociImporter.java:81)
at ij.IJ.runUserPlugIn(IJ.java:195)
at ij.IJ.runPlugIn(IJ.java:160)
at ij.Executer.runCommand(Executer.java:128)
at ij.Executer.run(Executer.java:64)
at java.lang.Thread.run(Thread.java:619)


If i select one (series 1) here is the error message i get:
ImageJ 1.47v; Java 1.6.0_20 [64-bit]; Windows NT (unknown) 6.2; 29MB of 2986MB (<1%)

java.lang.IllegalArgumentException: Array size too large: 99959 x 70344 x 1
at loci.common.DataTools.safeMultiply32(DataTools.java:888)
at loci.common.DataTools.allocate(DataTools.java:862)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:157)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:305)
at loci.formats.DimensionSwapper.openBytes(DimensionSwapper.java:248)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:305)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:305)
at loci.plugins.util.ImageProcessorReader.openProcessors(ImageProcessorReader.java:190)
at loci.plugins.in.ImagePlusReader.readProcessors(ImagePlusReader.java:416)
at loci.plugins.in.ImagePlusReader.readPlanes(ImagePlusReader.java:380)
at loci.plugins.in.ImagePlusReader.readImage(ImagePlusReader.java:277)
at loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:238)
at loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:216)
at loci.plugins.in.ImagePlusReader.openImagePlus(ImagePlusReader.java:114)
at loci.plugins.in.Importer.readPixels(Importer.java:150)
at loci.plugins.in.Importer.run(Importer.java:89)
at loci.plugins.LociImporter.run(LociImporter.java:81)
at ij.IJ.runUserPlugIn(IJ.java:195)
at ij.IJ.runPlugIn(IJ.java:160)
at ij.Executer.runCommand(Executer.java:128)
at ij.Executer.run(Executer.java:64)
at java.lang.Thread.run(Thread.java:619)

IF i create an "image view" in imageScope:

loci.formats.UnknownFormatException: Unknown file format: D:\Lab\Aperio images\try40X.sis
at loci.formats.ImageReader.getReader(ImageReader.java:192)
at loci.plugins.in.ImportProcess.createBaseReader(ImportProcess.java:596)
at loci.plugins.in.ImportProcess.initializeReader(ImportProcess.java:472)
at loci.plugins.in.ImportProcess.execute(ImportProcess.java:142)
at loci.plugins.in.Importer.showDialogs(Importer.java:141)
at loci.plugins.in.Importer.run(Importer.java:79)
at loci.plugins.LociImporter.run(LociImporter.java:81)
at ij.IJ.runUserPlugIn(IJ.java:195)
at ij.IJ.runPlugIn(IJ.java:160)
at ij.Executer.runCommand(Executer.java:128)
at ij.Executer.run(Executer.java:64)
at java.lang.Thread.run(Thread.java:619)
loci.formats.UnknownFormatException: Unknown file format: D:\Lab\Aperio images\try40X.sis
at loci.formats.ImageReader.getReader(ImageReader.java:192)
at loci.plugins.in.ImportProcess.createBaseReader(ImportProcess.java:596)
at loci.plugins.in.ImportProcess.initializeReader(ImportProcess.java:472)
at loci.plugins.in.ImportProcess.execute(ImportProcess.java:142)
at loci.plugins.in.Importer.showDialogs(Importer.java:141)
at loci.plugins.in.Importer.run(Importer.java:79)
at loci.plugins.LociImporter.run(LociImporter.java:81)
at ij.IJ.runUserPlugIn(IJ.java:195)
at ij.IJ.runPlugIn(IJ.java:160)
at ij.Executer.runCommand(Executer.java:128)
at ij.Executer.run(Executer.java:64)
at java.lang.Thread.run(Thread.java:619)

OK, so given that i have imageScope from aperio and ImageJ, how could i fix this ?
Thank you :D :D :D :D :D :D
benjaminek
 
Posts: 2
Joined: Fri Mar 21, 2014 6:58 pm
Top

Re: Image J Bioformat SVS or SVI image

Postby mlinkert » Sun Mar 23, 2014 9:04 pm

IF i open all series :
ImageJ 1.47v; Java 1.6.0_20 [64-bit]; Windows NT (unknown) 6.2; 29MB of 2986MB (<1%)

java.lang.NegativeArraySizeException
at loci.formats.MinMaxCalculator.openBytes(MinMaxCalculator.java:263)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:305)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:305)
at loci.plugins.util.ImageProcessorReader.openProcessors(ImageProcessorReader.java:190)
at loci.plugins.in.ImagePlusReader.readProcessors(ImagePlusReader.java:416)
at loci.plugins.in.ImagePlusReader.readPlanes(ImagePlusReader.java:380)
at loci.plugins.in.ImagePlusReader.readImage(ImagePlusReader.java:277)
at loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:238)
at loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:216)
at loci.plugins.in.ImagePlusReader.openImagePlus(ImagePlusReader.java:114)
at loci.plugins.in.Importer.readPixels(Importer.java:150)
at loci.plugins.in.Importer.run(Importer.java:89)
at loci.plugins.LociImporter.run(LociImporter.java:81)
at ij.IJ.runUserPlugIn(IJ.java:195)
at ij.IJ.runPlugIn(IJ.java:160)
at ij.Executer.runCommand(Executer.java:128)
at ij.Executer.run(Executer.java:64)
at java.lang.Thread.run(Thread.java:619)


If i select one (series 1) here is the error message i get:
ImageJ 1.47v; Java 1.6.0_20 [64-bit]; Windows NT (unknown) 6.2; 29MB of 2986MB (<1%)

java.lang.IllegalArgumentException: Array size too large: 99959 x 70344 x 1
at loci.common.DataTools.safeMultiply32(DataTools.java:888)
at loci.common.DataTools.allocate(DataTools.java:862)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:157)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:305)
at loci.formats.DimensionSwapper.openBytes(DimensionSwapper.java:248)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:305)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:305)
at loci.plugins.util.ImageProcessorReader.openProcessors(ImageProcessorReader.java:190)
at loci.plugins.in.ImagePlusReader.readProcessors(ImagePlusReader.java:416)
at loci.plugins.in.ImagePlusReader.readPlanes(ImagePlusReader.java:380)
at loci.plugins.in.ImagePlusReader.readImage(ImagePlusReader.java:277)
at loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:238)
at loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:216)
at loci.plugins.in.ImagePlusReader.openImagePlus(ImagePlusReader.java:114)
at loci.plugins.in.Importer.readPixels(Importer.java:150)
at loci.plugins.in.Importer.run(Importer.java:89)
at loci.plugins.LociImporter.run(LociImporter.java:81)
at ij.IJ.runUserPlugIn(IJ.java:195)
at ij.IJ.runPlugIn(IJ.java:160)
at ij.Executer.runCommand(Executer.java:128)
at ij.Executer.run(Executer.java:64)
at java.lang.Thread.run(Thread.java:619)


Both of those error messages indicate that the image contains more than 2GB of pixel data. ImageJ cannot open more than 2GB in a single image plane, so you will need to use the "Crop on import" option in the "Bio-Formats Import Options" window to open a smaller section of the image(s).

IF i create an "image view" in imageScope:

loci.formats.UnknownFormatException: Unknown file format: D:\Lab\Aperio images\try40X.sis
at loci.formats.ImageReader.getReader(ImageReader.java:192)
at loci.plugins.in.ImportProcess.createBaseReader(ImportProcess.java:596)
at loci.plugins.in.ImportProcess.initializeReader(ImportProcess.java:472)
at loci.plugins.in.ImportProcess.execute(ImportProcess.java:142)
at loci.plugins.in.Importer.showDialogs(Importer.java:141)
at loci.plugins.in.Importer.run(Importer.java:79)
at loci.plugins.LociImporter.run(LociImporter.java:81)
at ij.IJ.runUserPlugIn(IJ.java:195)
at ij.IJ.runPlugIn(IJ.java:160)
at ij.Executer.runCommand(Executer.java:128)
at ij.Executer.run(Executer.java:64)
at java.lang.Thread.run(Thread.java:619)
loci.formats.UnknownFormatException: Unknown file format: D:\Lab\Aperio images\try40X.sis
at loci.formats.ImageReader.getReader(ImageReader.java:192)
at loci.plugins.in.ImportProcess.createBaseReader(ImportProcess.java:596)
at loci.plugins.in.ImportProcess.initializeReader(ImportProcess.java:472)
at loci.plugins.in.ImportProcess.execute(ImportProcess.java:142)
at loci.plugins.in.Importer.showDialogs(Importer.java:141)
at loci.plugins.in.Importer.run(Importer.java:79)
at loci.plugins.LociImporter.run(LociImporter.java:81)
at ij.IJ.runUserPlugIn(IJ.java:195)
at ij.IJ.runPlugIn(IJ.java:160)
at ij.Executer.runCommand(Executer.java:128)
at ij.Executer.run(Executer.java:64)
at java.lang.Thread.run(Thread.java:619)


.sis image view files are not currently supported by Bio-Formats; if you would like to be able to open these files, it would be helpful if you could send one or more sample datasets to:

http://qa.openmicroscopy.org.uk/qa/upload
User avatar
mlinkert
Team Member
 
Posts: 353
Joined: Fri May 29, 2009 2:12 pm
Location: Southwest Wisconsin
Top

Re: Image J Bioformat SVS or SVI image

Postby benjaminek » Mon Mar 24, 2014 12:53 am

Thank you for your help!
benjaminek
 
Posts: 2
Joined: Fri Mar 21, 2014 6:58 pm
Top
Post a reply

Return to User Discussion [Legacy]

Who is online

Users browsing this forum: No registered users and 1 guest

Powered by phpBB © 2000, 2002, 2005, 2007 phpBB Group