bioformats appears broken in latest update

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bioformats appears broken in latest update

Aryeh Weiss
In the latest update, my attempts to open oib or nd2 files result in:

(Fiji Is Just) ImageJ 2.0.0-rc-68/1.52d; Java 1.8.0_172 [64-bit]; Mac OS
X 10.13.5; 146MB of 9092MB (1%)

java.lang.NullPointerException
     at
org.scijava.nativelib.NativeLibraryUtil.getPlatformLibraryPath(NativeLibraryUtil.java:189)
     at
org.scijava.nativelib.NativeLibraryUtil.loadNativeLibrary(NativeLibraryUtil.java:308)
     at
loci.formats.services.JPEGTurboServiceImpl.<init>(JPEGTurboServiceImpl.java:107)
     at loci.formats.in.NDPIReader.<init>(NDPIReader.java:69)
     at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native
Method)
     at
sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
     at
sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
     at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
     at java.lang.Class.newInstance(Class.java:442)
     at loci.formats.ImageReader.<init>(ImageReader.java:129)
     at loci.formats.in.FilePatternReader.<init>(FilePatternReader.java:77)
     at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native
Method)
     at
sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
     at
sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
     at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
     at java.lang.Class.newInstance(Class.java:442)
     at loci.formats.ImageReader.<init>(ImageReader.java:129)
     at loci.plugins.util.LociPrefs.makeImageReader(LociPrefs.java:100)
     at
loci.plugins.in.ImportProcess.createBaseReader(ImportProcess.java:619)
     at
loci.plugins.in.ImportProcess.initializeReader(ImportProcess.java:485)
     at loci.plugins.in.ImportProcess.execute(ImportProcess.java:138)
     at loci.plugins.in.Importer.showDialogs(Importer.java:140)
     at loci.plugins.in.Importer.run(Importer.java:76)
     at loci.plugins.LociImporter.run(LociImporter.java:78)
     at ij.IJ.runUserPlugIn(IJ.java:228)
     at ij.IJ.runPlugIn(IJ.java:192)
     at ij.IJ.runPlugIn(IJ.java:181)
     at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:499)
     at HandleExtraFileTypes.run(HandleExtraFileTypes.java:72)
     at ij.IJ.runUserPlugIn(IJ.java:228)
     at ij.IJ.runPlugIn(IJ.java:192)
     at ij.IJ.runPlugIn(IJ.java:181)
     at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:515)
     at ij.io.Opener.openImage(Opener.java:369)
     at ij.io.Opener.openImage(Opener.java:242)
     at ij.io.Opener.open(Opener.java:109)
     at ij.io.Opener.openAndAddToRecent(Opener.java:291)
     at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:192)
     at ij.plugin.DragAndDrop.run(DragAndDrop.java:159)
     at java.lang.Thread.run(Thread.java:748)

This occurs also with a fresh download of fiji, with no extra update
sites installed.

I run macos 10.13.5, java 1.8.0_172

My last backup for my fiji is from 29 June, but it was working on
Friday, so something happened between then and now.

--aryeh

--
Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: 972-3-7384051


--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
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Re: bioformats appears broken in latest update

Herbie
Good day Aryeh,

there are a number of similar reports on the IJ-Forum but apparently all of
those in the know are enjoying their weekend or are on vacations.

Let's see how things look like on Monday.

Best

Herbie
_________________________________________

Aryeh Weiss wrote

> In the latest update, my attempts to open oib or nd2 files result in:
>
> (Fiji Is Just) ImageJ 2.0.0-rc-68/1.52d; Java 1.8.0_172 [64-bit]; Mac OS
> X 10.13.5; 146MB of 9092MB (1%)
>
> java.lang.NullPointerException
>      at
> org.scijava.nativelib.NativeLibraryUtil.getPlatformLibraryPath(NativeLibraryUtil.java:189)
>      at
> org.scijava.nativelib.NativeLibraryUtil.loadNativeLibrary(NativeLibraryUtil.java:308)
>      at
> loci.formats.services.JPEGTurboServiceImpl.
> <init>
> (JPEGTurboServiceImpl.java:107)
>      at loci.formats.in.NDPIReader.
> <init>
> (NDPIReader.java:69)
>      at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native
> Method)
>      at
> sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
>      at
> sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
>      at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
>      at java.lang.Class.newInstance(Class.java:442)
>      at loci.formats.ImageReader.
> <init>
> (ImageReader.java:129)
>      at loci.formats.in.FilePatternReader.
> <init>
> (FilePatternReader.java:77)
>      at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native
> Method)
>      at
> sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
>      at
> sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
>      at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
>      at java.lang.Class.newInstance(Class.java:442)
>      at loci.formats.ImageReader.
> <init>
> (ImageReader.java:129)
>      at loci.plugins.util.LociPrefs.makeImageReader(LociPrefs.java:100)
>      at
> loci.plugins.in.ImportProcess.createBaseReader(ImportProcess.java:619)
>      at
> loci.plugins.in.ImportProcess.initializeReader(ImportProcess.java:485)
>      at loci.plugins.in.ImportProcess.execute(ImportProcess.java:138)
>      at loci.plugins.in.Importer.showDialogs(Importer.java:140)
>      at loci.plugins.in.Importer.run(Importer.java:76)
>      at loci.plugins.LociImporter.run(LociImporter.java:78)
>      at ij.IJ.runUserPlugIn(IJ.java:228)
>      at ij.IJ.runPlugIn(IJ.java:192)
>      at ij.IJ.runPlugIn(IJ.java:181)
>      at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:499)
>      at HandleExtraFileTypes.run(HandleExtraFileTypes.java:72)
>      at ij.IJ.runUserPlugIn(IJ.java:228)
>      at ij.IJ.runPlugIn(IJ.java:192)
>      at ij.IJ.runPlugIn(IJ.java:181)
>      at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:515)
>      at ij.io.Opener.openImage(Opener.java:369)
>      at ij.io.Opener.openImage(Opener.java:242)
>      at ij.io.Opener.open(Opener.java:109)
>      at ij.io.Opener.openAndAddToRecent(Opener.java:291)
>      at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:192)
>      at ij.plugin.DragAndDrop.run(DragAndDrop.java:159)
>      at java.lang.Thread.run(Thread.java:748)
>
> This occurs also with a fresh download of fiji, with no extra update
> sites installed.
>
> I run macos 10.13.5, java 1.8.0_172
>
> My last backup for my fiji is from 29 June, but it was working on
> Friday, so something happened between then and now.
>
> --aryeh
>
> --
> Aryeh Weiss
> Faculty of Engineering
> Bar Ilan University
> Ramat Gan 52900 Israel
>
> Ph:  972-3-5317638
> FAX: 972-3-7384051
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html





--
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--
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Re: bioformats appears broken in latest update

Curtis Rueden
In reply to this post by Aryeh Weiss
Hi Aryeh,

Could you please try deleting jars/native-lib-loader-2.3.0.jar and
replacing it with jars/native-lib-loader-2.2.0.jar from your working
installation?

Regards,
Curtis


On Sat, Jul 7, 2018, 16:47 Aryeh Weiss <[hidden email]> wrote:

> In the latest update, my attempts to open oib or nd2 files result in:
>
> (Fiji Is Just) ImageJ 2.0.0-rc-68/1.52d; Java 1.8.0_172 [64-bit]; Mac OS
> X 10.13.5; 146MB of 9092MB (1%)
>
> java.lang.NullPointerException
>      at
>
> org.scijava.nativelib.NativeLibraryUtil.getPlatformLibraryPath(NativeLibraryUtil.java:189)
>      at
>
> org.scijava.nativelib.NativeLibraryUtil.loadNativeLibrary(NativeLibraryUtil.java:308)
>      at
>
> loci.formats.services.JPEGTurboServiceImpl.<init>(JPEGTurboServiceImpl.java:107)
>      at loci.formats.in.NDPIReader.<init>(NDPIReader.java:69)
>      at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native
> Method)
>      at
>
> sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
>      at
>
> sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
>      at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
>      at java.lang.Class.newInstance(Class.java:442)
>      at loci.formats.ImageReader.<init>(ImageReader.java:129)
>      at loci.formats.in
> .FilePatternReader.<init>(FilePatternReader.java:77)
>      at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native
> Method)
>      at
>
> sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
>      at
>
> sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
>      at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
>      at java.lang.Class.newInstance(Class.java:442)
>      at loci.formats.ImageReader.<init>(ImageReader.java:129)
>      at loci.plugins.util.LociPrefs.makeImageReader(LociPrefs.java:100)
>      at
> loci.plugins.in.ImportProcess.createBaseReader(ImportProcess.java:619)
>      at
> loci.plugins.in.ImportProcess.initializeReader(ImportProcess.java:485)
>      at loci.plugins.in.ImportProcess.execute(ImportProcess.java:138)
>      at loci.plugins.in.Importer.showDialogs(Importer.java:140)
>      at loci.plugins.in.Importer.run(Importer.java:76)
>      at loci.plugins.LociImporter.run(LociImporter.java:78)
>      at ij.IJ.runUserPlugIn(IJ.java:228)
>      at ij.IJ.runPlugIn(IJ.java:192)
>      at ij.IJ.runPlugIn(IJ.java:181)
>      at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:499)
>      at HandleExtraFileTypes.run(HandleExtraFileTypes.java:72)
>      at ij.IJ.runUserPlugIn(IJ.java:228)
>      at ij.IJ.runPlugIn(IJ.java:192)
>      at ij.IJ.runPlugIn(IJ.java:181)
>      at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:515)
>      at ij.io.Opener.openImage(Opener.java:369)
>      at ij.io.Opener.openImage(Opener.java:242)
>      at ij.io.Opener.open(Opener.java:109)
>      at ij.io.Opener.openAndAddToRecent(Opener.java:291)
>      at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:192)
>      at ij.plugin.DragAndDrop.run(DragAndDrop.java:159)
>      at java.lang.Thread.run(Thread.java:748)
>
> This occurs also with a fresh download of fiji, with no extra update
> sites installed.
>
> I run macos 10.13.5, java 1.8.0_172
>
> My last backup for my fiji is from 29 June, but it was working on
> Friday, so something happened between then and now.
>
> --aryeh
>
> --
> Aryeh Weiss
> Faculty of Engineering
> Bar Ilan University
> Ramat Gan 52900 Israel
>
> Ph:  972-3-5317638
> FAX: 972-3-7384051
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
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Re: bioformats appears broken in latest update

Aryeh Weiss
On 08/07/2018 3:54, Curtis Rueden wrote:
> Hi Aryeh,
>
> Could you please try deleting jars/native-lib-loader-2.3.0.jar and
> replacing it with jars/native-lib-loader-2.2.0.jar from your working
> installation?
yes -- that fixed it.

Thank you for your quick reply, on a Saturday night.

Best regards
--aryeh

>
> Regards,
> Curtis
>
>
> On Sat, Jul 7, 2018, 16:47 Aryeh Weiss <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>     In the latest update, my attempts to open oib or nd2 files result in:
>
>     (Fiji Is Just) ImageJ 2.0.0-rc-68/1.52d; Java 1.8.0_172 [64-bit];
>     Mac OS
>     X 10.13.5; 146MB of 9092MB (1%)
>
>     java.lang.NullPointerException
>          at
>     org.scijava.nativelib.NativeLibraryUtil.getPlatformLibraryPath(NativeLibraryUtil.java:189)
>          at
>     org.scijava.nativelib.NativeLibraryUtil.loadNativeLibrary(NativeLibraryUtil.java:308)
>          at
>     loci.formats.services.JPEGTurboServiceImpl.<init>(JPEGTurboServiceImpl.java:107)
>          at loci.formats.in.NDPIReader.<init>(NDPIReader.java:69)
>          at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native
>     Method)
>          at
>     sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
>          at
>     sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
>          at
>     java.lang.reflect.Constructor.newInstance(Constructor.java:423)
>          at java.lang.Class.newInstance(Class.java:442)
>          at loci.formats.ImageReader.<init>(ImageReader.java:129)
>          at loci.formats.in
>     <http://loci.formats.in>.FilePatternReader.<init>(FilePatternReader.java:77)
>          at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native
>     Method)
>          at
>     sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
>          at
>     sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
>          at
>     java.lang.reflect.Constructor.newInstance(Constructor.java:423)
>          at java.lang.Class.newInstance(Class.java:442)
>          at loci.formats.ImageReader.<init>(ImageReader.java:129)
>          at
>     loci.plugins.util.LociPrefs.makeImageReader(LociPrefs.java:100)
>          at
>     loci.plugins.in.ImportProcess.createBaseReader(ImportProcess.java:619)
>          at
>     loci.plugins.in.ImportProcess.initializeReader(ImportProcess.java:485)
>          at loci.plugins.in.ImportProcess.execute(ImportProcess.java:138)
>          at loci.plugins.in.Importer.showDialogs(Importer.java:140)
>          at loci.plugins.in.Importer.run(Importer.java:76)
>          at loci.plugins.LociImporter.run(LociImporter.java:78)
>          at ij.IJ.runUserPlugIn(IJ.java:228)
>          at ij.IJ.runPlugIn(IJ.java:192)
>          at ij.IJ.runPlugIn(IJ.java:181)
>          at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:499)
>          at HandleExtraFileTypes.run(HandleExtraFileTypes.java:72)
>          at ij.IJ.runUserPlugIn(IJ.java:228)
>          at ij.IJ.runPlugIn(IJ.java:192)
>          at ij.IJ.runPlugIn(IJ.java:181)
>          at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:515)
>          at ij.io.Opener.openImage(Opener.java:369)
>          at ij.io.Opener.openImage(Opener.java:242)
>          at ij.io.Opener.open(Opener.java:109)
>          at ij.io.Opener.openAndAddToRecent(Opener.java:291)
>          at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:192)
>          at ij.plugin.DragAndDrop.run(DragAndDrop.java:159)
>          at java.lang.Thread.run(Thread.java:748)
>
>     This occurs also with a fresh download of fiji, with no extra update
>     sites installed.
>
>     I run macos 10.13.5, java 1.8.0_172
>
>     My last backup for my fiji is from 29 June, but it was working on
>     Friday, so something happened between then and now.
>
>     --aryeh
>
>     --
>     Aryeh Weiss
>     Faculty of Engineering
>     Bar Ilan University
>     Ramat Gan 52900 Israel
>
>     Ph:  972-3-5317638
>     FAX: 972-3-7384051
>
>
>     --
>     ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: 972-3-7384051


--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
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Re: bioformats appears broken in latest update

Curtis Rueden
In reply to this post by Curtis Rueden
Hi Aryeh,

> yes -- that fixed it.

Thanks, I reverted the Java-8 update site to the
native-lib-loader-2.2.0.jar again, until we can investigate and fix this
new bug in 2.3.0.

Regards,
Curtis

--
Curtis Rueden
LOCI software architect - https://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/


On Sat, Jul 7, 2018 at 9:52 PM, Aryeh Weiss <[hidden email]> wrote:

> On 08/07/2018 3:54, Curtis Rueden wrote:
>
>> Hi Aryeh,
>>
>> Could you please try deleting jars/native-lib-loader-2.3.0.jar and
>> replacing it with jars/native-lib-loader-2.2.0.jar from your working
>> installation?
>>
> yes -- that fixed it.
>
> Thank you for your quick reply, on a Saturday night.
>
> Best regards
> --aryeh
>
>>
>> Regards,
>> Curtis
>>
>>
>> On Sat, Jul 7, 2018, 16:47 Aryeh Weiss <[hidden email] <mailto:
>> [hidden email]>> wrote:
>>
>>     In the latest update, my attempts to open oib or nd2 files result in:
>>
>>     (Fiji Is Just) ImageJ 2.0.0-rc-68/1.52d; Java 1.8.0_172 [64-bit];
>>     Mac OS
>>     X 10.13.5; 146MB of 9092MB (1%)
>>
>>     java.lang.NullPointerException
>>          at
>>     org.scijava.nativelib.NativeLibraryUtil.getPlatformLibraryPa
>> th(NativeLibraryUtil.java:189)
>>          at
>>     org.scijava.nativelib.NativeLibraryUtil.loadNativeLibrary(Na
>> tiveLibraryUtil.java:308)
>>          at
>>     loci.formats.services.JPEGTurboServiceImpl.<init>(JPEGTurboS
>> erviceImpl.java:107)
>>          at loci.formats.in.NDPIReader.<init>(NDPIReader.java:69)
>>          at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native
>>     Method)
>>          at
>>     sun.reflect.NativeConstructorAccessorImpl.newInstance(Native
>> ConstructorAccessorImpl.java:62)
>>          at
>>     sun.reflect.DelegatingConstructorAccessorImpl.newInstance(De
>> legatingConstructorAccessorImpl.java:45)
>>          at
>>     java.lang.reflect.Constructor.newInstance(Constructor.java:423)
>>          at java.lang.Class.newInstance(Class.java:442)
>>          at loci.formats.ImageReader.<init>(ImageReader.java:129)
>>          at loci.formats.in
>>     <http://loci.formats.in>.FilePatternReader.<init>(FilePatter
>> nReader.java:77)
>>
>>          at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native
>>     Method)
>>          at
>>     sun.reflect.NativeConstructorAccessorImpl.newInstance(Native
>> ConstructorAccessorImpl.java:62)
>>          at
>>     sun.reflect.DelegatingConstructorAccessorImpl.newInstance(De
>> legatingConstructorAccessorImpl.java:45)
>>          at
>>     java.lang.reflect.Constructor.newInstance(Constructor.java:423)
>>          at java.lang.Class.newInstance(Class.java:442)
>>          at loci.formats.ImageReader.<init>(ImageReader.java:129)
>>          at
>>     loci.plugins.util.LociPrefs.makeImageReader(LociPrefs.java:100)
>>          at
>>     loci.plugins.in.ImportProcess.createBaseReader(ImportProcess
>> .java:619)
>>          at
>>     loci.plugins.in.ImportProcess.initializeReader(ImportProcess
>> .java:485)
>>          at loci.plugins.in.ImportProcess.execute(ImportProcess.java:138)
>>          at loci.plugins.in.Importer.showDialogs(Importer.java:140)
>>          at loci.plugins.in.Importer.run(Importer.java:76)
>>          at loci.plugins.LociImporter.run(LociImporter.java:78)
>>          at ij.IJ.runUserPlugIn(IJ.java:228)
>>          at ij.IJ.runPlugIn(IJ.java:192)
>>          at ij.IJ.runPlugIn(IJ.java:181)
>>          at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:499)
>>          at HandleExtraFileTypes.run(HandleExtraFileTypes.java:72)
>>          at ij.IJ.runUserPlugIn(IJ.java:228)
>>          at ij.IJ.runPlugIn(IJ.java:192)
>>          at ij.IJ.runPlugIn(IJ.java:181)
>>          at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:515)
>>          at ij.io.Opener.openImage(Opener.java:369)
>>          at ij.io.Opener.openImage(Opener.java:242)
>>          at ij.io.Opener.open(Opener.java:109)
>>          at ij.io.Opener.openAndAddToRecent(Opener.java:291)
>>          at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:192)
>>          at ij.plugin.DragAndDrop.run(DragAndDrop.java:159)
>>          at java.lang.Thread.run(Thread.java:748)
>>
>>     This occurs also with a fresh download of fiji, with no extra update
>>     sites installed.
>>
>>     I run macos 10.13.5, java 1.8.0_172
>>
>>     My last backup for my fiji is from 29 June, but it was working on
>>     Friday, so something happened between then and now.
>>
>>     --aryeh
>>
>>     --     Aryeh Weiss
>>     Faculty of Engineering
>>     Bar Ilan University
>>     Ramat Gan 52900 Israel
>>
>>     Ph:  972-3-5317638
>>     FAX: 972-3-7384051
>>
>>
>>     --
>>     ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>>
> --
> Aryeh Weiss
> Faculty of Engineering
> Bar Ilan University
> Ramat Gan 52900 Israel
>
> Ph:  972-3-5317638
> FAX: 972-3-7384051
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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