Cell detection improvement

edit

I would create a small application which counts the number of cells of a honey comb. (I'll count the number of covered and uncovered cells based on theirs color in the next step ...)

Most on uncovered cells are found but the covered and those which contains honey are still missing.

I would really appreciate if someone could help me how to improve my current contour detection solution. Any ideas, suggestions are welcomed.

This the input image: C:\fakepath\IMG_20150825_133836.jpg

Here is my code:

#include "opencv2/highgui/highgui.hpp"
#include "opencv2/imgproc/imgproc.hpp"
#include <iostream>
#include <stdio.h>
#include <stdlib.h>

using namespace cv;
using namespace std;

int main(int /*argc*/, char** /*argv*/)
{
    Mat src; Mat src_gray; Mat canny_output;
    int thresh = 30;
    vector<vector<Point> > contours;
    vector<Vec4i> hierarchy;

    src = imread("IMG_20150825_133836.jpg", 1);

    cvtColor(src, src_gray, CV_BGR2GRAY);
    blur(src_gray, src_gray, Size(3, 3));
    Canny(src_gray, canny_output, thresh, thresh * 2, 3);
    /// Find contours
    findContours(canny_output, contours, hierarchy, CV_RETR_TREE, CV_CHAIN_APPROX_SIMPLE, Point(0, 0));
    /// Draw contours
    Mat drawing = Mat::zeros(canny_output.size(), CV_8UC3);
    for (int i = 0; i< contours.size(); i++)
    {
        if (contourArea(contours[i]) > 100) {       //filter noise
            drawContours(drawing, contours, i, Scalar(255, 255, 255), -1, 8, hierarchy, 0, Point());
        }
    }
    namedWindow("Comb", CV_WINDOW_AUTOSIZE);
    imshow("Comb", drawing);
    waitKey(0);
    return(0);
}

The current output is: