MATLAB:
I=imread('P_Falc_thin2.jpg');
figure;enter image description here
imshow(I)
I_comp=imcomplement(I); %takes complement of image
figure;
imshow(I_comp)


%Filter cells from background
level=graythresh(I_comp);
BW=im2bw(I_comp,level);
figure;
imshow(BW);



cells = bwareafilt(BW, [20 700000]); %size exclusion by area will only keep images within these parameters
figure;
imshow(cells)
cells2 = bwareaopen(cells,100);
figure;
imshow(cells2)
maskedImage = I_comp;
maskedImage(~cells) = 0; %set whatever is not within this size black
mask=I_comp>100;
[enter image description here][1]

MATLAB:
I=imread('P_Falc_thin2.jpg');
figure;enter image description here
imshow(I)
I_comp=imcomplement(I); %takes complement of image
figure;
imshow(I_comp)


%Filter cells from background
level=graythresh(I_comp);
BW=im2bw(I_comp,level);
figure;
imshow(BW);



cells = bwareafilt(BW, [20 700000]); %size exclusion by area will only keep images within these parameters
figure;
imshow(cells)
cells2 = bwareaopen(cells,100);
figure;
imshow(cells2)
maskedImage = I_comp;
maskedImage(~cells) = 0; %set whatever is not within this size black
mask=I_comp>100;



Java:


import java.util.Scanner;
import org.opencv.core.Core;
import org.opencv.core.Mat;

import org.opencv.core.CvType;
import org.opencv.core.Scalar;
import javax.swing.ImageIcon;
import javax.swing.JFrame;
import javax.swing.JLabel;


import org.opencv.core.*;
import org.opencv.imgcodecs.*; // imread, imwrite, etc
import org.opencv.imgproc.Imgproc;


public class ProcessImage {

    public static void main(String[] args) {
        System.loadLibrary("opencv_java320");

        //File name info:
        String file = "C:/Users/Nirali Patel/Desktop/Java/thinSmear1";
        String ext = ".jpg";
        String pathToFile = file+ext;

        // Mat is the image matrix
        Mat mat=Imgcodecs.imread(pathToFile, Imgcodecs.CV_LOAD_IMAGE_COLOR);
        LoadImage(file,ext,mat, "_Input");

        // Complement Image
        Mat mat_comp = mat;
        Core.bitwise_not(mat,mat_comp);
        Mat mat_grayscale = mat_comp;
        LoadImage(file,ext,mat_grayscale,"_Complement_Input");

        // GrayScale Image
        Imgproc.cvtColor(mat_comp, mat_grayscale, Imgproc.COLOR_RGB2GRAY,0);
        LoadImage(file,ext,mat_grayscale,"_inverted&grayscale");

        // threshold cells
        Mat mat_thresh = mat_comp;
        Imgproc.threshold(mat_thresh, mat_comp, 0, 255, Imgproc.THRESH_OTSU);
        LoadImage(file,ext,mat_thresh,"thresh");


        //Remove background noise
        Mat mat_morph = mat_thresh;
        Imgproc.blur(mat_grayscale, mat_morph, new Size (20,20));
        LoadImage(file,ext,mat_morph, "morph");

        //Edge Detection
        Mat mat_edges= mat_morph;
        Imgproc.Canny(mat_edges, mat_morph, 5, 75, 3, true);
        LoadImage(file,ext,mat_edges, "Edges");

        //Close Image
        Mat dilateElement = Imgproc.getStructuringElement(Imgproc.MORPH_CROSS, new Size(30, 10));
        Mat erodeElement = Imgproc.getStructuringElement(Imgproc.MORPH_ELLIPSE, new Size(7, 1));

        Mat mat_dilate= mat_edges;
        Imgproc.dilate(mat_dilate, mat_edges, dilateElement);
        LoadImage(file,ext, mat_dilate, "Dilate Cells");

        Mat mat_erode=mat_dilate;
        Imgproc.erode(mat_dilate, mat_edges, erodeElement);
        LoadImage(file,ext, mat_erode, "Erode Cells");
        // create temporary image that will hold the mask
        //Mat mask_image( your_image.size(), CV_8U, Scalar(0));
        // draw your contour in mask
        //drawContours(mask_image, contours, ind, Scalar(255), CV_FILLED);
        // copy only non-zero pixels from your image to original image
        //your_image.copyTo(original_image, mask_image);



    }








    public static void LoadImage(String imgStr,
            String ext,Mat m, String name){
        String new_img_name = imgStr+name+ext;
        Imgcodecs.imwrite(new_img_name,m);
        JFrame frame = new JFrame(name);
        frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);

        frame.setLocationRelativeTo(null);

        // Inserts the image icon
        ImageIcon I = new ImageIcon(new_img_name);

        frame.setSize(I.getIconWidth()+10,I.getIconHeight()+35);
        // Draw the Image data into the BufferedImage
        JLabel label1 = new JLabel(" ", I, JLabel.CENTER);
        frame.getContentPane().add(label1);

        frame.validate();
        frame.setVisible(true);

    }

}