Posted by
Josh Klein on
URL: http://imagej.273.s1.nabble.com/Neurite-tracer-tp3692383p3692384.html
What do you mean by 'manually remove the seedling'? I could measure the individual seedlings just using the wand tool. I'm trying to avoid treating each seedling separately, but if it comes to that, I'll just use the wand.
Is there a program that can outline and label (number) elements on an image?
Thanks again,
josh
--- On Thu, 5/28/09, Gabriel Lapointe <
[hidden email]> wrote:
From: Gabriel Lapointe <
[hidden email]>
Subject: Re: Neurite tracer
To:
[hidden email]
Date: Thursday, May 28, 2009, 8:45 AM
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>
>
>
>
>
>