Issue with ImageJ plug-in (simple neurite tracer) compatability

[Thomas S]

Hi all, 

I am new to ICY, having been given a introductory training session today, so apologies if this question is rather mundane.

I am attempting to trace a line across a 2d image generally following the most intense pixels. I have attempted to generate a ROI using the built-in ICY plugin KymographTracker, but am not having too much success, so decided to use the imageJ simple neurite tracer plugin instead. However, when I click on the imageJ pane to open the simple neurite tracer i receive the following message : 

Plugin or class not found: "Simple_Neurite_Tracer"

(java.lang.ClassNotFoundException: Simple_Neurite_Tracer)

I have moved other plugins from FIJI to the Icy IJ folder and they work fine, it is just this plugin which I am having a problem with. 

I was wondering if anybody had any advice or knows of a different way to trace a ROI in an image following the most intense pixels?

Thanks in advance

[Stephane]

Hi Thomas,

Sorry for replying that late... I have no idea why this plugin is not correctly loaded when you're using it from Icy.
Indeed if i try to launch it from Icy with Java 7 i see the class could not be loaded because it requires java 8 but if i use java 8 then i obtain the same error message than you : class not found... that doesn't really make sense as the class is there obviously.
I guess it's a problem with ClassLoader but as we don't have access to the source we can't really understand why..

Did you try active contour ? It's not really made for neurone but it can somehow follow high intensity depending the settings...

Best,

- Stephane

[Curtis Rueden]

Hi Stephane and everyone,

> if i use java 8 then i obtain the same error message than you : class

> not found... that doesn't really make sense as the class is there

> obviously.

Note that the Simple_Neurite_Tracer class lives in a package called "tracing" [1] so its fully qualified class name should be "tracing.Simple_Neurite_Tracer"; this is what its plugins.config declares too [2].

Maybe that is related somehow? Is there a way to get a full stack trace for this error, instead of just the message?

Regards,

Curtis

[1] https://github.com/fiji/Simple_Neurite_Tracer/blob/Simple_Neurite_Tracer-3.1.3/src/main/java/tracing/Simple_Neurite_Tracer.java

[2] https://github.com/fiji/Simple_Neurite_Tracer/blob/Simple_Neurite_Tracer-3.1.3/src/main/resources/plugins.config#L4

--

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/

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[Stephane]

Hi Curtis,

Indeed there is something wrong about that. I just tested in ImageJ (not Fiji) and we obtain the same error (Icy embed ImageJ, not Fiji). So this is a bug with ImageJ which is not present in Fiji...

- Stephane

Le lundi 3 juillet 2017 16:10:41 UTC+2, Curtis Rueden a écrit :

Hi Stephane and everyone,

> if i use java 8 then i obtain the same error message than you : class

> not found... that doesn't really make sense as the class is there

> obviously.

Note that the Simple_Neurite_Tracer class lives in a package called "tracing" [1] so its fully qualified class name should be "tracing.Simple_Neurite_Tracer"; this is what its plugins.config declares too [2].

Maybe that is related somehow? Is there a way to get a full stack trace for this error, instead of just the message?

Regards,

Curtis

[1] https://github.com/fiji/Simple_Neurite_Tracer/blob/Simple_Neurite_Tracer-3.1.3/src/main/java/tracing/Simple_Neurite_Tracer.java

[2] https://github.com/fiji/Simple_Neurite_Tracer/blob/Simple_Neurite_Tracer-3.1.3/src/main/resources/plugins.config#L4

--

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/

[Ma Ja]

Hi all,

any workarounds? I am having the same problem...

Max

[Stephane]

Unfortunately that is more a problem from ImageJ now... I guess the plugin has been wrote for Fiji initially ?

- Stephane