Posted by
Gabriel Lapointe on
URL: http://imagej.273.s1.nabble.com/Neurite-tracer-tp3692383p3692388.html
Hi Josh,
Just brainstorming here but, maybe something like this could be a
starting point.
* Threshold and make the image binary
* Manually remove the seedling
* run Process > Binary > Skeletonize
* run Analyze > Analyze particles.
Assuming that the root or not entangled each particle would be a single
root length by a single pixel width. I'm not aware of a way to
automatically measure the length in ImageJ. however, the length could
therefore be *estimated* as either:
area/pixel_width OR perimeter/2-1pixel_width
My understanding of how ImageJ measure the perimeter, I would bet that
the second method can give very bad results.
Good luck,
Gabriel Lapointe
Josh Klein wrote:
> I did look at that. What I am trying to do is measure individual roots on young seedlings, where there are anywhere from 10-25 seedlings in on image. The roots are not yet all tangled with each other, so I really want a program that identifies individual roots and measures the length. I can do this manually, of course, on the screen using ImageJ measuring wands, but my students and I both are getting repetitive strain injury! Both neurite tracing programs measure _all_ the neurites at once, and I want automatic definition
> of individual entities.
> Thanks for your suggestion; any thoughts on the more closely defined problem above?
> Cheers,
> josh
> --- On Thu, 5/28/09, Albert Cardona <
[hidden email]> wrote:
>
>
> From: Albert Cardona <
[hidden email]>
> Subject: Re: Neurite tracer
> To:
[hidden email]
> Date: Thursday, May 28, 2009, 3:40 AM
>
>
> Josh Klein wrote:
>
>> I am trying to use the Neurite Tracer plugin. When I get to the step
>> for "Open images for setting threshold", the program won't let me
>> select images from a file. It only recognizes the folders themselves,
>> which of course are not .tif images that the plugin requires, and then it tosses me out of the
>> program.
>> Suggestions leading to success would be appreciated.
>>
>>
>
>
> Josh,
>
> Did you have a look at the "Simple Neurite Tracer" by Mark Longair?
>
>
http://pacific.mpi-cbg.de/wiki/index.php/Simple_Neurite_Tracer>
http://homepages.inf.ed.ac.uk/s9808248/imagej/tracer/>
>
> Albert
>
> -- Albert Cardona
>
http://albert.rierol.net>
>
>
>
>
>