LOCI won't open large .vsi files

[Olivier Burri]

Dear all,

I'm having trouble opening the largest resolution image from a slide scanner, in -vsi format.

The files are a total of 500MB on the hard drive which isn't much.

I can open 6144x12800 file but the 27136x62976 file gives me the error below.

While we're on the subject, is there a plugin for navigating large tiles like these in a "google maps" mode? Like a virtual stack but with chunks of tiles being loaded as we pan or zoom though the images?

Thanks!

Oli

java.lang.reflect.InvocationTargetException
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
        at java.lang.reflect.Method.invoke(Method.java:597)
        at ij.Command.runPlugIn(Command.java:146)
        at ij.Command.runCommand(Command.java:95)
        at ij.Executer.run(Executer.java:64)
        at java.lang.Thread.run(Thread.java:662)
Caused by: java.lang.ArrayIndexOutOfBoundsException
        at loci.formats.in.CellSensReader.openBytes(CellSensReader.java:235)
        at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:183)
        at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:175)
        at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:180)
        at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:304)
        at loci.formats.DimensionSwapper.openBytes(DimensionSwapper.java:249)
        at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:304)
        at loci.formats.MinMaxCalculator.openBytes(MinMaxCalculator.java:260)
        at loci.formats.MinMaxCalculator.openBytes(MinMaxCalculator.java:252)
        at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:292)
        at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:292)
        at loci.plugins.util.ImageProcessorReader.openProcessors(ImageProcessorReader.java:188)
        at loci.plugins.in.ImagePlusReader.readProcessors(ImagePlusReader.java:414)
        at loci.plugins.in.ImagePlusReader.readPlanes(ImagePlusReader.java:378)
        at loci.plugins.in.ImagePlusReader.readImage(ImagePlusReader.java:275)
        at loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:236)
        at loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:214)
        at loci.plugins.in.ImagePlusReader.openImagePlus(ImagePlusReader.java:112)
        at loci.plugins.in.Importer.readPixels(Importer.java:148)
        at loci.plugins.in.Importer.run(Importer.java:87)
        at loci.plugins.LociImporter.run(LociImporter.java:79)
        at ij.IJ.runUserPlugIn(IJ.java:183)
        at ij.IJ.runPlugIn(IJ.java:150)
        ... 8 more



Olivier Burri
Engineer, Development in Image Processing
BioImaging and Optics platform (PTBIOP)

[Vitali Khvatkov-2]

Oli,

We specialize in handling virtual slides , so some points from experience:

- If your image is compressed than size on disk is not representative. E.g
JPEG at 90% compression may take 500BM on disk by easily over 2GB  in
memory which will crash your x32 application. JPEG compression is typical
case with slide scanners. I don remember about Olympus specifically but I'm
sure this is the case because typical slide @20x is about 3.5GB before
compression.

- As for viewing: you have to have either a specialty viewer or server or
have your slide "pre-cut" into image tile pyramid to view in browsers. I
don't believe ImageJ has this component today.

On Viewers (for local viewing)
- Aperio ImageScope is free Windows application for local slide viewing. It
does not support .vsi, but it supports Hamamatsu .ndpi .vms .vmu slides and
if I recall correctly Olympus got technology from Hamamatsu (or vise versa)
and you may have option to save slide in Hamamatsu format
- Zoomify is a Flash based application, they can view JPEG image pyramids
(not  Olympus slides)
- Microsoft has free *Microsoft HD Viewer  (support their own format)*

On Servers. There are just few  Hardware independent companies that provide
servers
- We provide both web cloud solutions and private servers (more at
live.simagis.com)
- Aurora from Canada provides deployed (not cloud) servers
- PathXL from Ireland is another provider

None of the vendors above, Including us, handle Olympus .vsi slides today.
But we are actively adding new formats to our server and if you send me
some sample slides we may be able to add this format to the library, in
which case you can use our free web service to view, share, and analyze
your slides online.

I hope it helps,
*
*
*
*
*Vitali Khvatkov*
Smart Imaging Technologies Co.
Office: [phone]
www.simagis.com


On Fri, Mar 9, 2012 at 8:09 AM, Burri Olivier <[hidden email]> wrote:

> Dear all,
>
> I'm having trouble opening the largest resolution image from a slide
> scanner, in -vsi format.
>
> The files are a total of 500MB on the hard drive which isn't much.
>
> I can open 6144x12800 file but the 27136x62976 file gives me the error
> below.
>
> While we're on the subject, is there a plugin for navigating large tiles
> like these in a "google maps" mode? Like a virtual stack but with chunks of
> tiles being loaded as we pan or zoom though the images?
>
> Thanks!
>
> Oli
>
> java.lang.reflect.InvocationTargetException
>        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>        at
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
>        at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
>        at java.lang.reflect.Method.invoke(Method.java:597)
>        at ij.Command.runPlugIn(Command.java:146)
>        at ij.Command.runCommand(Command.java:95)
>        at ij.Executer.run(Executer.java:64)
>        at java.lang.Thread.run(Thread.java:662)
> Caused by: java.lang.ArrayIndexOutOfBoundsException
>        at loci.formats.in.CellSensReader.openBytes(CellSensReader.java:235)
>        at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:183)
>        at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:175)
>        at
> loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:180)
>        at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:304)
>        at
> loci.formats.DimensionSwapper.openBytes(DimensionSwapper.java:249)
>        at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:304)
>        at
> loci.formats.MinMaxCalculator.openBytes(MinMaxCalculator.java:260)
>        at
> loci.formats.MinMaxCalculator.openBytes(MinMaxCalculator.java:252)
>        at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:292)
>        at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:292)
>        at
> loci.plugins.util.ImageProcessorReader.openProcessors(ImageProcessorReader.java:188)
>        at
> loci.plugins.in.ImagePlusReader.readProcessors(ImagePlusReader.java:414)
>        at
> loci.plugins.in.ImagePlusReader.readPlanes(ImagePlusReader.java:378)
>        at
> loci.plugins.in.ImagePlusReader.readImage(ImagePlusReader.java:275)
>        at
> loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:236)
>        at
> loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:214)
>        at
> loci.plugins.in.ImagePlusReader.openImagePlus(ImagePlusReader.java:112)
>        at loci.plugins.in.Importer.readPixels(Importer.java:148)
>        at loci.plugins.in.Importer.run(Importer.java:87)
>        at loci.plugins.LociImporter.run(LociImporter.java:79)
>        at ij.IJ.runUserPlugIn(IJ.java:183)
>        at ij.IJ.runPlugIn(IJ.java:150)
>        ... 8 more
>
>
>
> Olivier Burri
> Engineer, Development in Image Processing
> BioImaging and Optics platform (PTBIOP)

--
*Vitali Khvatkov*
Smart Imaging Technologies Co.
Office: [phone]
Direct: [phone]
[hidden email]
www.simagis.com

[Melissa Linkert-2]

Hi Oli,

> I'm having trouble opening the largest resolution image from a slide scanner, in -vsi format.
>
> The files are a total of 500MB on the hard drive which isn't much.
>
> I can open 6144x12800 file but the 27136x62976 file gives me the error below.

Would you be willing to send the problematic dataset to the Bio-Formats
developers?  I think I have sent you instructions previously on how to
do this, but if not let me know and I will send them privately.

Regards,
-Melissa

On Fri, Mar 09, 2012 at 02:09:29PM +0000, Burri Olivier wrote:

> Dear all,
>
> I'm having trouble opening the largest resolution image from a slide scanner, in -vsi format.
>
> The files are a total of 500MB on the hard drive which isn't much.
>
> I can open 6144x12800 file but the 27136x62976 file gives me the error below.
>
> While we're on the subject, is there a plugin for navigating large tiles like these in a "google maps" mode? Like a virtual stack but with chunks of tiles being loaded as we pan or zoom though the images?
>
> Thanks!
>
> Oli
>
> java.lang.reflect.InvocationTargetException
> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
> at java.lang.reflect.Method.invoke(Method.java:597)
> at ij.Command.runPlugIn(Command.java:146)
> at ij.Command.runCommand(Command.java:95)
> at ij.Executer.run(Executer.java:64)
> at java.lang.Thread.run(Thread.java:662)
> Caused by: java.lang.ArrayIndexOutOfBoundsException
> at loci.formats.in.CellSensReader.openBytes(CellSensReader.java:235)
> at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:183)
> at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:175)
> at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:180)
> at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:304)
> at loci.formats.DimensionSwapper.openBytes(DimensionSwapper.java:249)
> at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:304)
> at loci.formats.MinMaxCalculator.openBytes(MinMaxCalculator.java:260)
> at loci.formats.MinMaxCalculator.openBytes(MinMaxCalculator.java:252)
> at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:292)
> at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:292)
> at loci.plugins.util.ImageProcessorReader.openProcessors(ImageProcessorReader.java:188)
> at loci.plugins.in.ImagePlusReader.readProcessors(ImagePlusReader.java:414)
> at loci.plugins.in.ImagePlusReader.readPlanes(ImagePlusReader.java:378)
> at loci.plugins.in.ImagePlusReader.readImage(ImagePlusReader.java:275)
> at loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:236)
> at loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:214)
> at loci.plugins.in.ImagePlusReader.openImagePlus(ImagePlusReader.java:112)
> at loci.plugins.in.Importer.readPixels(Importer.java:148)
> at loci.plugins.in.Importer.run(Importer.java:87)
> at loci.plugins.LociImporter.run(LociImporter.java:79)
> at ij.IJ.runUserPlugIn(IJ.java:183)
> at ij.IJ.runPlugIn(IJ.java:150)
> ... 8 more
>
>
>
> Olivier Burri
> Engineer, Development in Image Processing
> BioImaging and Optics platform (PTBIOP)