calculating area and perimeter for pap-smear image

Greetings,

I want to calculate the area and perimeter of the nucleus of image i have attached here. i have tried some of the codes, but i cant get it. please help me with the code for calculating the area and perimeter.

Thank you in advance.

Answer 1

[Turlough Hughes]

There are numerous ways you could segment the nucleus, I elected here to threshold based on R,G,B values in the image. To work out appropriate threshold values you can use the color thresholder app (I have already done that in this case). You will have to change the filename and you may also change rgb threshold values as you please. Note the thresholds are set to accept values less than rThresh, gThresh, bThresh.

I suggest you also look at the definitions for the properties obtained using the regionprops function. You will need to have some scale in terms of pixels per mm or pixels per micrometer to determine meaningful perimeter and area quantites.

% Parameters
% RGB threshold values
rThresh = 130;
gThresh = 130;
bThresh = 150;
% filename
filename = 'vidhya.bmp';

% Setup
fontSize = 16;
figure('Units', 'Normalized', 'OuterPosition', [0 0 1 1])

% Load & show image
A = imread(filename); 
subplot(2,2,1), imshow(A)
title('Original Image','fontSize',fontSize)

% Implent thresholding
B = A(:,:,1)<rThresh & A(:,:,2)<gThresh & A(:,:,3)<bThresh;

% Display result of threshold
subplot(2,2,2), imshow(B)
title(sprintf('Values less than threshold (R:%d, G:%d, B:%d)', ...
    rThresh,gThresh,bThresh),'fontSize',fontSize)

% Filter out all but the largest area & display results
C = bwareafilt(B,1);
subplot(2,2,3), imshow(C)
title('Largest area selected','fontSize',fontSize)

% Fill the area so all pixels inside are true
D = imfill(C,'holes');

% Get Area and Perimeter
props = regionprops(D,'Area','Perimeter');

% Show results
subplot(2,2,4), imshow(D);
title(sprintf('Final region (area filled) \n Area: %dpx     Perimeter: %4.2fpx', ...
    props.Area,props.Perimeter),'fontSize',fontSize)

[vidhya v]

Thank you so much sir for your quick response. I will try this.

Thank you

[Turlough Hughes]

No problem. Happy to help :)

[vidhya v]

Hello sir,

I tried the code and it works well for color image. As per project, In GUI i have separately created pushbuttons for each steps (preprocess, segmenation, feature extraction etc.).

But for calculating the area, perimeter and diameter I have to call the segmented image in pushbutton for AREA. I tried but cannot able to load the image. Please consider my request and help me with the code.

Hereby I have attached my code

Thanking you

[Image Analyst]

You have this:

global im im2 I feature img_comp_s img_comp_s1

and you say you "cannot able to load the image". I'm not sure which one of those is the segmented image you're trying to load. Let's say it's im. So if im is your segmented (binary, logical) image, then to get the area(s) you just do:

props = regionprops(im, 'Area');
allAreas = [props.Area];

If it's not im, then replace that with whichever of those variables is your segmented image.

[vidhya v]

'img_comp_s' is the image i have to calculate the features, sir

[Image Analyst]

Then like I said, if img_comp_s is your binary image mask, do:

props = regionprops(img_comp_s, 'Area');
allAreas = [props.Area];

Attach your .fig file if you want more help.

[vidhya v]

function area_Callback(hObject, eventdata, handles)

% hObject handle to area (see GCBO)

% eventdata reserved - to be defined in a future version of MATLAB

% handles structure with handles and user data (see GUIDATA)

global im im2 I feature img_comp_s img_comp_s1

axes(handles.axes2);

feature = findobj(handles.axes2, 'type', 'image');

handles.ImgData2 = img_comp_s;

guidata(hObject,handles);

J = imcrop(img_comp_s);

bin = imbinarize(img_comp_s);

props = regionprops(bin,'Area');

allarea = [props.Area];

This is my code i tried sir. The problem is I have to show the calculated value of area in the edit text if i click the pushbutton of 'AREA'

please suggest me how can i get it done.

Thanking you.