MATLAB: How to characterize these cells by area and diameter

image processingImage Processing Toolboximage segmentation

I have this picture:

The particles of interest are labeled in red. I would like to quantify these labeled images by area and diameter.

For reference, the above image came from this image:

I think there might be a way to take this image and contrast the white to the black and come up with an area and diameter, but I'm not really.

As always,

Thanks for your time,

Respectfully,

Tushar

Best Answer

Related Solutions

MATLAB: How to quantify this image based on area and perimeter

Hi Tushar

this is John BG <mailto:jgb2012@sky.com jgb2012@sky.com>

1. acquiring image

A=imread('001.jpg');
h1=figure(1);imshow(A)
ax=gca

even the object of interest has low illumination, so the binarization threshold set low, at 12 only:

A1=A(:,:,1);
% A1=imbinarize(A,10);
A1(A1>10)=255;A1(A1<12)=0;
figure;imshow(A1)

3.-

Getting boundaries of all the objects

[B,L]=bwboundaries(A1);
perim=[];
for k=1:1:size(B,1)
    perim=[perim size(B{k,:},1)];
end

4.-

Capturing the object of interest, because it has by far the longest perimeter:

B1_cell=B(find(perim==max(perim)),:);
B1=B1_cell{:};
hold(ax,'all');
plot(ax,B1(:,2),B1(:,1),'r','LineWidth',2)

5.-

the length of the perimeter, in pixels

Obj_perim_length=size(B1,1)   % perimeter length in pixels

6.- now for the area

    xp=B1(:,2);
    yp=B1(:,1);
    D=zeros(size(A1));
    for k=1:1:numel(xp)
      D(yp(k),xp(k))=1;
    end
    % figure;imshow(D);axd=gca;
    D2=imfill(D,'holes')
    figure;imshow(D2)

    obj_area =
       5.207962500000000e+04
    obj_area/(size(A1,1)*size(A1,2)) =
     0.259624444156414

the area is of 52k pixels, about a quarter of the input image rectangle, if one can accurately get a scale of the window, then translation from pixels to mm, cm, microns, whatever .. is straight forward.

f you find this answer useful would you please be so kind to consider marking my answer as Accepted Answer?

To any other reader, if you find this answer useful please consider clicking on the thumbs-up vote link

thanks in advance for time and attention

John BG

<mailto:jgb2012@sky.com jgb2012@sky.com>

additional comments:

What I tried but either time consuming or more complex than the above solution:

1. inpolygon with all points of the initial image against the found perimeter:

% too time consuming, it almost crashes MATLAB twice
[in,on]=inpolygon(yq,xq,B1(:,2),B1(:,1));
in1=find(in>0);
for k=1:1:length(in)
    plot(ax,xq(in1(k)),yq(in1(k)),'b*');
end

2. Define an alphashape and then apply command area

% alphasape awkwardly defines the shapes along the perimeter
% leaving almost all inside hollow, therefore the resulting area is almost that of a thin perimeter strip, not of the whole inside
shp1=alphaShape(B1(:,2),B1(:,1))
figure;plot(shp1)
area_obj1=area(shp1)
area_obj1/(size(A1,1)*size(A1,2))
% hold all
% for k = 1:length(B)
%    boundary = B{k};
%    plot(boundary(:,2), boundary(:,1),'r', 'LineWidth', 2)
% end

too sketchy without filtering first, that it's been already done above

A2=del2(double(A1));figure;imshow(A2)

Laplacian gets the correct perimeter, but along with many other 'false' perimeters, thus requiring filtering before applying del2.

MATLAB: Index in position 1 exceeds array bounds

If imfindcircles finds less than 5 circles you are going to error.

A = imread('circle.png');
imshow(A);
[centers, radii, metric] = imfindcircles(A,[15 30]);
a=max(5,length(centers));
centersStrong5 = centers(1:a,:); 
radiiStrong5 = radii(1:a);
metricStrong5 = metric(1:a);
viscircles(centersStrong5, radiiStrong5,'EdgeColor','b');

Best Answer

Related Solutions

MATLAB: How to quantify this image based on area and perimeter

MATLAB: Index in position 1 exceeds array bounds

Related Question