This program quantifies the colones grown in a 3D agar matrix from a greyscale image, by recurising through directories with images. It outputs both the number of colonies in each image as well as its cross sectional area in a .csv. In addition it makes a smaller quality control image to visually verify performance
Since this program is much older than the beta-gal counter, you have to fine tune performance via the global variables in the top of the script itself
-m --magnification: Microscope magnification - 4x or 10x. Default is 4x
-s --stained: Stained -s flag will use an algorithm optimized for stained colonies. No flag uses the unstained algorithm
-i --input: Directory where images are located. Defaults to current directory
-t --testing: Will display intermediate QC images for fine tuning parameters.
Python 2.7.14
- cv2 v3.4.0 (opencv)
- numpy v1.14.2
- matplotlib v2.2.3
- optparse v1.5.3