Scion frame grabber plugins under OS X 10.4

[Jeff Hardin]

Dear friends,

I have been a happy user of the Mac OS 9 versions of Scion's ImageJ  
plugins for their digitizing boards (we have more than one AG-5),  
which I have adapted for my own 4d acquisition suite. I'm now trying  
to get the plugins working under Mac OS X 10.4 (Tiger), under Java VM  
1.4.2. I have tried my modified plugins, Scion's plugins bundled with  
the old ImageJ 1.23, and their newer plugins under ImageJ 1.34 for  
use with their newer FG7 board. They all throw exceptions related to  
the creation and/or conversion of Simages (a Scion data format) to  
ImageJ ImagePlus objects. This means that the "Capture Grayscale"  
plugin fails at this point, and the "Export" option within the Live  
Capture plugin fails with a general exception.  The plugins compile,  
but there seems to be something wacky at this point.

I've provided the ImageJ exception and the console error,  
respectively, below. Note that I can see a live image using the Live  
Capture plugin, I can adjust the board's settings, save these  
options, and toggle visibility of the toolbar and status bar. Adrian  
Daerr's JNIAkiz plugin works, but because it doesn't provide the  
ability to modify the gain and contrast settings and averaging  
settings, it are not optimal. Moreover, the Scion plugins do exactly  
what I'd like under OS 9.

Thanks in advance for your help!

Cheers,

Jeff

Error messages:

(1) When running the  "Capture Grayscale" plugin using the pre-
packaged Scion for ImageJ (ImageJ 1.34s):

java.lang.NoClassDefFoundError: ij/ImagePlus
at scion.ij.ScionIJTools.createSimage(ScionIJTools.java:87)
at Capture_Grayscale.capture_image(Capture_Grayscale.java:134)
at Capture_Grayscale.run(Capture_Grayscale.java:78)
at ij.IJ.runUserPlugIn(IJ.java:265)
at ij.IJ.runPlugIn(IJ.java:109)
at ij.Executer.runPlugIn(Executer.java:169)
at ij.Executer.runCommand(Executer.java:131)
at ij.Executer.run(Executer.java:63)
at java.lang.Thread.run(Thread.java:552)


(2) When running the "Live Capture" plugin and invoking the "Export  
Image" command (from the menu or the icon in the Toolbar) using the  
pre-packaged Scion for ImageJ (ImageJ 1.34s):

apple.awt.EventQueueExceptionHandler Caught Throwable :  
java.lang.NoClassDefFoundError: ij/ImagePlus
java.lang.NoClassDefFoundError: ij/ImagePlus
        at scion.ij.ScionIJTools.createImagePlus(ScionIJTools.java:126)
        at Live_Capture.export_image(Live_Capture.java:150)
        at scion.cd.LiveWin.live_command(LiveWin.java:995)
        at scion.cd.LiveWin.actionPerformed(LiveWin.java:841)
        at java.awt.MenuItem.processActionEvent(MenuItem.java:589)
        at java.awt.MenuItem.processEvent(MenuItem.java:548)
        at java.awt.MenuComponent.dispatchEventImpl(MenuComponent.java:285)
        at java.awt.MenuComponent.dispatchEvent(MenuComponent.java:273)
        at java.awt.EventQueue.dispatchEvent(EventQueue.java:458)
        at java.awt.EventDispatchThread.pumpOneEventForHierarchy
(EventDispatchThread.java:234)
        at java.awt.EventDispatchThread.pumpEventsForHierarchy
(EventDispatchThread.java:184)
        at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:
178)
        at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:
170)
        at java.awt.EventDispatchThread.run(EventDispatchThread.java:100)


----------------------------------------------
Jeff Hardin
Professor, Department of Zoology
Director, Biology Core Curriculum
University of Wisconsin
1117 W. Johnson St.
Madison, WI 53706
voice: [phone]
fax: [phone]
email: [hidden email]

[Jeff Hardin]

Hi folks,

After a lot of class path troubleshooting, I realized I'd made a dumb  
mistake, and had an extra copy of scion.jar in System/Library/Java/
Extensions. ImageJ was using that copy, and so it couldn't find  
ij.jar. Once I trashed that, all was well.

Sorry for the silly mistake, and hopefully if someone does the same  
thing at some point in the future they'll find the relevant post.

Cheers,

Jeff

----------------------------------------------
Jeff Hardin
Professor, Department of Zoology
Director, Biology Core Curriculum
University of Wisconsin
1117 W. Johnson St.
Madison, WI 53706
voice: [phone]
fax: [phone]
email: [hidden email]


On Sep 13, 2006, at 11:00 PM, IMAGEJ automatic digest system wrote:

> Date:    Wed, 13 Sep 2006 13:00:39 -0500
> From:    Jeff Hardin <[hidden email]>
> Subject: Scion frame grabber plugins under OS X 10.4
>
> Dear friends,
>
> I have been a happy user of the Mac OS 9 versions of Scion's ImageJ
> plugins for their digitizing boards (we have more than one AG-5),
> which I have adapted for my own 4d acquisition suite. I'm now trying
> to get the plugins working under Mac OS X 10.4 (Tiger), under Java VM
> 1.4.2. I have tried my modified plugins, Scion's plugins bundled with
> the old ImageJ 1.23, and their newer plugins under ImageJ 1.34 for
> use with their newer FG7 board. They all throw exceptions related to
> the creation and/or conversion of Simages (a Scion data format) to
> ImageJ ImagePlus objects. This means that the "Capture Grayscale"
> plugin fails at this point, and the "Export" option within the Live
> Capture plugin fails with a general exception.  The plugins compile,
> but there seems to be something wacky at this point.

[lechristophe]

Hi everybody,

I'm playing with the different selection tools and I discovered the
"line width" option for straight line selections. Neat feature ! I was
wondering if it's possible to draw segmented line or freehand line
selection with such a given pixel width, but the basic tools are just
one pixel wide lines... Is there a way to do it ? If not, it would be a
nice addition in terms of tool consistency and also very useful for
people that measure signals along features such as dendrites etc...

Christophe Leterrier

Equipe Canaux Ioniques et Polarité Neuronale :: Bénédicte Dargent
INSERM UMR 641
Laboratoire Neurobiologie des Canaux Ioniques :: Mike Seagar
Institut Jean Roche :: Université de la Méditerranée
51, boulevard Pierre Dramard :: 13919 Marseille Cedex 20
Téléphone 04 91 69 89 30 :: Fax [phone]
site web : http://ifrjr.nord.univ-mrs.fr
email : [hidden email]

[Gabriel Landini]

On Friday 15 September 2006 15:30, Christophe Leterrier wrote:
> I'm playing with the different selection tools and I discovered the
> "line width" option for straight line selections. Neat feature ! I was
> wondering if it's possible to draw segmented line or freehand line
> selection with such a given pixel width, but the basic tools are just
> one pixel wide lines... Is there a way to do it ?

select line width
draw freehand line
press "D"

G.

[ctrueden]

Hi Jeff,

I recently discovered that support libraries for plugins do not have
to be in the JRE extensions folder (e.g.,
/System/Library/Java/Extensions), but actually work fine if placed in
the ImageJ plugins folder with the relevant plugin (I hadn't realized
ImageJ's plugin class loader was that smart).

Actually, the pure plugins folder approach is better on Mac OS X,
because if you place a library in the JRE extensions folder, all its
dependencies must also be placed in the extensions folder, or else
Mac's Java will not find the dependencies properly (even if they are
present in the classpath).

To reflect these issues, I have changed the installation instructions
for Bio-Formats to indicate all JARs should go into the plugins
folder.

-Curtis

On 9/14/06, Jeff Hardin <[hidden email]> wrote:

> Hi folks,
>
> After a lot of class path troubleshooting, I realized I'd made a dumb
> mistake, and had an extra copy of scion.jar in System/Library/Java/
> Extensions. ImageJ was using that copy, and so it couldn't find
> ij.jar. Once I trashed that, all was well.
>
> Sorry for the silly mistake, and hopefully if someone does the same
> thing at some point in the future they'll find the relevant post.
>
> Cheers,
>
> Jeff
>
> ----------------------------------------------
> Jeff Hardin
> Professor, Department of Zoology
> Director, Biology Core Curriculum
> University of Wisconsin
> 1117 W. Johnson St.
> Madison, WI 53706
> voice: [phone]
> fax: [phone]
> email: [hidden email]
>
>
> On Sep 13, 2006, at 11:00 PM, IMAGEJ automatic digest system wrote:
>
> > Date:    Wed, 13 Sep 2006 13:00:39 -0500
> > From:    Jeff Hardin <[hidden email]>
> > Subject: Scion frame grabber plugins under OS X 10.4
> >
> > Dear friends,
> >
> > I have been a happy user of the Mac OS 9 versions of Scion's ImageJ
> > plugins for their digitizing boards (we have more than one AG-5),
> > which I have adapted for my own 4d acquisition suite. I'm now trying
> > to get the plugins working under Mac OS X 10.4 (Tiger), under Java VM
> > 1.4.2. I have tried my modified plugins, Scion's plugins bundled with
> > the old ImageJ 1.23, and their newer plugins under ImageJ 1.34 for
> > use with their newer FG7 board. They all throw exceptions related to
> > the creation and/or conversion of Simages (a Scion data format) to
> > ImageJ ImagePlus objects. This means that the "Capture Grayscale"
> > plugin fails at this point, and the "Export" option within the Live
> > Capture plugin fails with a general exception.  The plugins compile,
> > but there seems to be something wacky at this point.
>

[lechristophe]

But this draws on my image !

I want to get a n pixel wide selection, not changing the value of my
pixels (which is what pressing D is doing)

Gabriel Landini a écrit :

> On Friday 15 September 2006 15:30, Christophe Leterrier wrote:
>> I'm playing with the different selection tools and I discovered the
>> "line width" option for straight line selections. Neat feature ! I was
>> wondering if it's possible to draw segmented line or freehand line
>> selection with such a given pixel width, but the basic tools are just
>> one pixel wide lines... Is there a way to do it ?
>
> select line width
> draw freehand line
> press "D"
>
> G.
>

[Gabriel Landini]

On Friday 15 September 2006 15:46, Christophe Leterrier wrote:
> But this draws on my image !
>
> I want to get a n pixel wide selection, not changing the value of my
> pixels (which is what pressing D is doing)

Select the "brush ROI" selection in the Elliptical ROI icon. (right click)
Double click to set the diameter on the same icon.
Draw slowly on the image.

G.

[lechristophe]

Thanks for the ellipse workaround !

Anyway I think what I want has already been asked, see

http://www.nabble.com/changing-the-linewidth-of-lines-drawn-through-segmented-and-freehand-line-tools---Bug-%28-%29-tf1559788.html

so I'll also wait, as "This is a feature that will be added in a future
version of ImageJ", to quote Wayne Rasband. He also suggested using the
"Straighten" plugin.

Thanks everybody for your help,

Christophe

Gabriel Landini a écrit :

> On Friday 15 September 2006 15:46, Christophe Leterrier wrote:
>> But this draws on my image !
>>
>> I want to get a n pixel wide selection, not changing the value of my
>> pixels (which is what pressing D is doing)
>
> Select the "brush ROI" selection in the Elliptical ROI icon. (right click)
> Double click to set the diameter on the same icon.
> Draw slowly on the image.
>
> G.
>

[Perry, Griffin M]

Dear Listserv,

I work at UTHSCSA (UT Health Science Center San Antonio), and I've just found out there's a UTHSCSA ImageTool.  I'm an ImageJ user until I die (or at least get fired from this job)!  I'm just curious to see if anyone's used it and what the pros and cons of UTHSCSA ImageTool are.

I hope it's not blasphemy to discuss this on the ImageJ listserv.  hehehe...

-Griffin Perry
Research Assistant
UTHSCSA

Repeat:  ImageJ user until I die (or at least get fired from this job)!

[Dale Thayer]

Last time I asked someone at UTHSCSA (perhaps 6 months ago), they do not
support the code anymore, and haven't for at least 4 years.





"Perry, Griffin M" <[hidden email]>
Sent by: ImageJ Interest Group <[hidden email]>
09/15/2006 03:25 PM
Please respond to
ImageJ Interest Group <[hidden email]>


To
[hidden email]
cc

Subject
Curiosity on UTHSCSA ImageTool






Dear Listserv,

I work at UTHSCSA (UT Health Science Center San Antonio), and I've just
found out there's a UTHSCSA ImageTool.  I'm an ImageJ user until I die (or
at least get fired from this job)!  I'm just curious to see if anyone's
used it and what the pros and cons of UTHSCSA ImageTool are.

I hope it's not blasphemy to discuss this on the ImageJ listserv.
hehehe...

-Griffin Perry
Research Assistant
UTHSCSA

Repeat:  ImageJ user until I die (or at least get fired from this job)!