nroldanf / colonies

Automatic system for colony counting using Digital Image Processing.

Brief Description of the Algorithm Used

Automatic system for colony counting using DIP techniques.

Process employed so far:

1. Grayscale conversion.

2. Linear contrast enhancement.

3. Determination of the petri-dish centers. 3.1. Edge detection using the Canny method. 3.2. Dilation with a diamond-shaped structuring element to better define the circular shapes of the Petri dish wells. 3.3. Cross-correlation with generated binary circular templates. 3.4. Finding the centers of the wells by locating them using the petri-dish radius.

4. Petri-dish segmentation: verifying all pixels that are within a circle with a specified average radius using the previously obtained centers.

5. Thresholding: determining a threshold using Otsu's method, which is scaled by a factor equal to the average of the image, and then applying this threshold to the image.

6. Segmentation of the colonies from the edges using Euclidean distance in the CIE Lab color space.

7. Elimination of colonies that do not have more than 50 cells using geometric properties of the regions.

8. Labeling and counting: regions with certain connectivity are labeled and then counted.