How to draw 50 equally distributed radii on a spherical image?

Hi,

I have fluorescent images from cell spheroids taken at different time points, and I would like to calculate the radial distribution of fluorescence for each time point. I have read a paper that briefly describes how to do this (https://pubs.acs.org/doi/full/10.1021/mp500002y); however, they do not provide the code for their custom algorithm. Therefore I decided to divide the problem into smaller steps as described in the paper, and my first challenge is to draw 50 equally spaced radii on the spherical microscopy images I have. I have no idea how to do this and therefore need your help. Could you please explain how I can do this on matlab?

Answer 1

[Image Analyst]

See attached demos that get values radially from a center point. Adapt as needed.

[Ceylan]

Thank you so much for your answer but I have already found this code from previous threads. This code still does not help me divide a spherical object into 50 equal radii. I still don't know how to do this after looking at this code, so adapting is a far away thing right now. Could you please help me understand how I can, from a chosen center point, draw 50 equal radii to the edges of a spherical object? Thank you in advance.

[Image Analyst]

First provide your code for creating the original spherical shell.

[Ceylan Sonmez]

Hi,

I am doing this for a friend of mine so I have been slightly slow but I would appreciate it if you could continue helping me on this.

So I read in my image that contains a single spherical green fluorescent blob. Then, adapting some of your code (calibration) and also your 2D radial distribution code, I identify the center point and then using the below modified code I draw the 50 equally distributed radial lines on the image:

i = 0:7.2:360; for j = 1:length(i) lineLength = 350; angle = i(j); centerX(1) = xcenter; centerY(1) = ycenter; centerX(2) = centerX(1) + lineLength * cosd(angle); centerY(2) = centerY(1) + lineLength * sind(angle); hold on; plot(centerX, centerY,'b-'); grid on; end

From this point onwards, my aim is to get the pixel intensities along each line and get an average pixel intensity for each line, followed by integrating average profiles from all lines to get total fluorescence of the whole sphere.

For this, I am trying to use the improfile function, and I am trying to provide the x and y coordinates of the lines above, so that I can get the intensities and RGB values in these specific points. I don't want to provide a N, as I want to get per pixel, which according to the explanation, this is what the function does if N is not provided.

My current problem is that I have all coordinates in matrices and my understanding is that the improfile function is not taking these as co-ordinates. Therefore, while my input is of length 51, I get CX, CY intensity values for 2000 points.

How should my input to the improfile be such that I can get pixel intensities along each 50 radii? I am really stuck. Or do you think there is a more appropriate function than improfile?

Your help is very much appreciated.

Kind regards.

[Image Analyst]

The code doesn't even run, so I quit at that point.

[Ceylan Sonmez]

The code runs. It's probably because you have not entered any value for xcenter and ycenter. In my code, before this section of the code, I click in the middle of the image, and therefore have these values at xcenter= 553 and ycenter = 270.

If you enter those values the code works but this is just part of the code so normally the output of the code is on an image. Should I provide the full code and upload a sample image?

[Ceylan Sonmez]

Providing the code again, with only minor addition to store all centerX and CenterY values

centerXf=[]; centerYf=[]; i = 0:7.2:360; for j = 1:length(i) lineLength = 350; angle = i(j); centerX(1) = xcenter; centerY(1) = ycenter; centerX(2) = centerX(1) + lineLength * cosd(angle); centerY(2) = centerY(1) + lineLength * sind(angle); hold on; plot(centerX, centerY,'b-'); grid on; centerXf(j,:)=centerX; centerYf(j,:)=centerY; end

[Image Analyst]

http://www.mathworks.com/matlabcentral/answers/13205#answer_18099

>> test
Undefined function or variable 'xcenter'.
Error in test (line 1)
centerXf=[]; centerYf=[]; i = 0:7.2:360; for j = 1:length(i) lineLength = 350; angle = i(j); centerX(1) = xcenter;
centerY(1) = ycenter; centerX(2) = centerX(1) + lineLength * cosd(angle); centerY(2) = centerY(1) + lineLength *
sind(angle); hold on; plot(centerX, centerY,'b-'); grid on; centerXf(j,:)=centerX; centerYf(j,:)=centerY; end

[Ceylan Sonmez]

Can you please use words to describe what the issue is? I already answered above that for xcenter the value that has to be entered is 553 and for ycenter its 270.

Once those values are provided the code runs fine.

Providing the code again assuming this is what you meant with the above response:

 centerXf=[];
 centerYf=[];
 i = 0:7.2:360;
 for j =  1:length(i)
   lineLength = 350;
   angle = i(j);
   centerX(1) = xcenter;
   centerY(1) = ycenter;
   centerX(2) = centerX(1) + lineLength * cosd(angle);
   centerY(2) = centerY(1) + lineLength * sind(angle);
   hold on;
   plot(centerX, centerY,'b-');
   grid on;
   centerXf(j,:)=centerX;
   centerYf(j,:)=centerY;
end

[Ceylan Sonmez]

Could you please let me know if you are unwilling to be helpful?