Mesh plot threshold in MatLab

Question

I am using an algorithm to determine a threshold for image analysis of nuclei in MATLAB. This algorithm measures all the pixel intensities within a nucleus and calculates a value that is used as a cutoff to distinguish background noise from foreground. I know how to apply this value to the image of the nuclei to see what effect the cutoff has, but I would like to apply the threshold to a mesh plot. By chance does anyone know how to do this I cannot post images yet but I have added example code of my image analysis

example image of nucleus

% First I load image
i = imread('nucleus.tif')
% I calculate the value of the threshold using my algorithm using my function
ci99 = getCI99('nucleus.tif')
% say for example that the calculated value is 100. I would apply this threshold to the image of the nucleus with the following command
imshow(picture , [ 100, inf]) % The resulting image only shows pixels at and above the calculated threshold.

I use the following code to make a mesh plot of a nucleus

% Mesh Plot
I=imread('nucleus.tif');
[x,y]=size(I);
X=1:x;
Y=1:y;
[xx,yy]=meshgrid(Y,X);
i=im2double(I);
figure;mesh(xx,yy,i);
colorbar
figure;imshow(i)

I am trying to apply the cutoff to the mesh plot analogous to the way I apply the threshold to the original image.

I would really appreciate any help.

Thanks

Potter Potter · Accepted Answer · 2013-11-20T21:37:28

check out the Matlab clim function

you should be able to do this with:

clim([min_threshold max_threshold]);

you can also access particular plots by holding on to axis handles (kinda like pointers)

fig1 = figure;
ax1  = mesh(xx,yy,i);
colorbar;

fig2 = figure;
ax2  = imshow(i);

set(ax1, 'clim', [100, inf]);

holding on to the axis handles lets you set parameters on any plot at any time, rather than only dealing with the last one you were working with.

Last note: try the image function rather than imshow. its not exactly the same thing, but you might find that you don't need to use the image processing toolbox at all.

Mesh plot threshold in MatLab

1 Answers