Analyze particles and show circles?

classic Classic list List threaded Threaded
3 messages Options
Reply | Threaded
Open this post in threaded view
|

Analyze particles and show circles?

JCortex
Hello,
I have thresholded images of Nissl-stained cortical sections that I need to
process.
Essentially, I need to sort the cells/objects by size and then create an
overlay/second image of the sorted objects, but instead of displaying the
objects, I need it to display filled circles (of a uniform size) at the
location of each identified object.
The closest I've come to achieving this so far with the program is to use
'analyze particles', select my size range, and then show either 'ellipses',
'masks', or 'overlay masks'. 'Ellipses' is the closest to what I need except
they are ellipses, not filled circles, and they all have varying sizes,
whereas I need to be able to set a uniform size for all sorted objects.  
Is there any way to achieve this?
Thank you



--
Sent from: http://imagej.1557.x6.nabble.com/

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
Reply | Threaded
Open this post in threaded view
|

Re: Analyze particles and show circles?

Straub, Volko A. (Dr.)
Not sure why you require the same size circles for all objects, but once you have created your masks, you could erode the masks to their ultimate single point. You could then either collect the coordinates of each point and draw circles. An easier/quicker approach would be to to dilate the points with a circular structuring element to the size you want.
The code below illustrates this for the 'Blobs' image. The diameter of the final circles is determined by the radius of the mean filter (I used the mean filter as the Binary Dilate doesn't create circles due to the use of a 3x3 structuring element).
Hope this helps.
Volko

run("Blobs (25K)");
setAutoThreshold("Default");
setOption("BlackBackground", true);
run("Convert to Mask");
run("Watershed");
run("Convert to Mask");
run("Ultimate Points");
setThreshold(1, 255);
run("Convert to Mask");
run("Mean...", "radius=3");
setThreshold(1, 255);
run("Convert to Mask");

________________________________
From: JCortex <[hidden email]>
Sent: 19 October 2018 17:23:30
To: [hidden email]
Subject: Analyze particles and show circles?

Hello,
I have thresholded images of Nissl-stained cortical sections that I need to
process.
Essentially, I need to sort the cells/objects by size and then create an
overlay/second image of the sorted objects, but instead of displaying the
objects, I need it to display filled circles (of a uniform size) at the
location of each identified object.
The closest I've come to achieving this so far with the program is to use
'analyze particles', select my size range, and then show either 'ellipses',
'masks', or 'overlay masks'. 'Ellipses' is the closest to what I need except
they are ellipses, not filled circles, and they all have varying sizes,
whereas I need to be able to set a uniform size for all sorted objects.
Is there any way to achieve this?
Thank you



--
Sent from: http://imagej.1557.x6.nabble.com/

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
Reply | Threaded
Open this post in threaded view
|

Re: Analyze particles and show circles?

Straub, Volko A. (Dr.)
In reply to this post by JCortex
Sorry, forgot to attached the macro code to my previous post. Here it is:


run("Blobs (25K)");
setAutoThreshold("Default");
setOption("BlackBackground", true);
run("Convert to Mask");
run("Watershed");
run("Convert to Mask");
run("Ultimate Points");
setThreshold(1, 255);
run("Convert to Mask");
run("Mean...", "radius=3");
setThreshold(1, 255);
run("Convert to Mask");


________________________________
From: JCortex <[hidden email]>
Sent: 19 October 2018 17:23:30
To: [hidden email]
Subject: Analyze particles and show circles?

Hello,
I have thresholded images of Nissl-stained cortical sections that I need to
process.
Essentially, I need to sort the cells/objects by size and then create an
overlay/second image of the sorted objects, but instead of displaying the
objects, I need it to display filled circles (of a uniform size) at the
location of each identified object.
The closest I've come to achieving this so far with the program is to use
'analyze particles', select my size range, and then show either 'ellipses',
'masks', or 'overlay masks'. 'Ellipses' is the closest to what I need except
they are ellipses, not filled circles, and they all have varying sizes,
whereas I need to be able to set a uniform size for all sorted objects.
Is there any way to achieve this?
Thank you



--
Sent from: http://imagej.1557.x6.nabble.com/

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html