Recommended Sholl Analysis Plugin?

[aavery]

Hi Everyone,
 
I am looking for an ImageJ plugin to perform Sholl analysis on neuron dendritic arbors.  I have heard that ImageJ can be used for this type of analysis.
 
I found an ImageJ plugin called "Sholl analysis" at
 
http://imagejdocu.tudor.lu/doku.php?id=plugin:analysis:asa:start
 
This plugin was developed by Tiago Ferreira and Tom Maddock and it looks like it would do the job nicely.  I have even found in the listserve archive questions from users of this plugin, and these questions were answered by Tiago Ferreira.  However, I cannot find the jar or class file for this plugin.  If anyone knows if it exists and/or where to locate the plugin file, please let me know.  I could not find a jar file download at the page listed above.
 
Other plugins I have come across:
 NeuronJ: can trace neurons but does not appear capable of Sholl analysis.
 Simple Neurite Tracer: appears capable of Sholl analysis but is listed as a Fiji plugin.  Can a Fiji plugin be run on ImageJ?
 
Any help for this ImageJ newbie would be appreciated.
 
Thanks!
Adam


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[Tiago Ferreira-2]

Hi Adam,
I really apologize for that.

On 2013.01.13, at 12:56 , Adam wrote:
> I found an ImageJ plugin called "Sholl analysis" at
> http://imagejdocu.tudor.lu/doku.php?id=plugin:analysis:asa:start

> However, I cannot find the jar or class file for this plugin.

This page should have been updated ages ago.
I'm committed to finish it, I just wish I had more time for it.

I am really sorry it gives the impression of abandonware, it is quite the
contrary: You can follow the development of "Sholl Analysis" on github:
<https://github.com/downloads/tferr/ASA/>.

To use it:
  1. Download bitmap_sholl.jar and place it in your plugins folder
     <https://github.com/downloads/tferr/ASA/bitmap_sholl.jar>
  2. Re-start IJ/Fiji or run Help>Refresh Menus
  3. The plugin will be available under "Analyze>Sholl Analysis..."
  4. The plugin also installs a sample image ("File>Open Samples>ddaC neuron")
     that you can use to get acquainted with the analysis

> Simple Neurite Tracer: appears capable of Sholl analysis but is listed as a Fiji
> plugin. Can a Fiji plugin be run on ImageJ?

Sure. As stated multiple times on this list, Fiji _is_ ImageJ. Note, however,
that you will have to manually install and maintain all the dependencies that
those plugins require if you want to use them outside Fiji. You will loose so
much time in doing it, that you will soon appreciate that you will be just doing
(in an extremely inefficient matter) what the powerful Fiji built-in updater does
already for you.

If you are confused about ImageJ distributions, this article may help:
<http://developer.imagej.net/faq/21#t21n141>

Note that Simple Neurite Tracer performs Sholl on traced arbors. Our
implementation performs Sholl directly on bitmap images.

Best,
-tiago

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[aavery]

Thanks Tiago.  Just tried out the plugin and it works great.  

Regards,
Adam

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[dscho]

Hi Adam,

On Sun, 13 Jan 2013, Adam wrote:

> Can a Fiji plugin be run on ImageJ?

Fiji Is Just ImageJ. So: yes.

Ciao,
Johannes

P.S.: See also
http://developer.imagej.net/what-difference-between-imagej-imagej2-imagejdev-imagejx-imageja-etc

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