> Well I assumed that the roots originate from some center point that is
> big and will produce weird thing in the skeletonization. Beside if the
> center point is still there, the results would be the sum of all the
> roots origination from that point.
>
> So what I meant is that you would have to remove that center point, a
> simple elliptical selection and a clear will do the trick and is faster
> than the whole measurements with the wand ( it might be possible to do
> it automatically but I can't say for sure without seeing an image).
>
> Analyze particle with the "show count mask" option enable will give you
> an numbered outline of objects.
>
> Gabriel
>
> Josh Klein wrote:
>
>> 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>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>
>>
>>
>>
>>
indeed it would make sens to see some of your images. The problem