Neurite tracer
Locked
 
|
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 Klein |
|
|
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 |
|
|
Albert Cardona <[hidden email]> wrote:
> > 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 Please note that if you are going to try that out, the version in the last major Fiji release has a bug that makes it unusable when you're using the 3D viewer option - if you run "Help > Update Fiji" you should get the latest version where that problem should be fixed. regards, mark |
|
|
In reply to this post by Josh Klein
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 |
|
|
Did you try NeuronJ from Erik Meijering ?
http://www.imagescience.org/meijering/software/neuronj/ Should make the manual tracing much more easy than a full-manual approach, it is similar to Simple Neurite Tracer but maybe a bit more easy to use. However if you want a full-auto method I don't know any besides "Neurite Tracer". Speaking of semi-automatic neurite tracings, would it be possible to have some kind of tool in ImageJ/Fiji that does what NeuronJ/Neurite Tracer does (a selection that follow neurite-like objects) but as a simple, dumbed-down ImageJ tool ? Something like a third option of Fiji's "lasso selection" tool ? Christophe On Thu, May 28, 2009 at 10:34 AM, Josh Klein <[hidden email]> 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 > > > > > |
|
|
In reply to this post by Josh Klein
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? > Yours is an image segmentation/recognition problem, for which there aren't any good generic solutions. Perhaps comercial packages like Neurolucida have implemented exactly the functionality you want, but I don't know. The problem is not impossible. You could get a computer science student to implement a solution during the course of a semester project, tailored to your data and analysis needs. Albert -- Albert Cardona http://albert.rierol.net |
|
|
In reply to this post by Josh Klein
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 > > > > > > |
|
|
In reply to this post by Josh Klein
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 > > > > > > |
|
|
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 >> >> >> >> >> >> >> > > > > > > |
|
|
Gabriel Lapointe a écrit :
> 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 reminds me vessel outgrowth from aortic rings or neurite outgrowth as observed in pc12 cells. There are some semi automatic procedures but as stated by Albert, the solution might be dedicated to your particular needs. Fabrice. -- Senger Fabrice |
«
Return to ImageJ
|
1 view|%1 views
| Free forum by Nabble | Edit this page |