Counting colony forming units (CFU) generated from cells plated onto solid agar. Left click to tag cells with red marker, right click to tag with yellow marker. Generates an image record of marked CFUs with red and yellow counts embedded into image record filename.

ColonyCounter.py

import pygame, os, sys
from pygame.locals import *

# Runs through all jpgs in current directory
# Opens each in turn, allowing user to click on image features
# Left clicking draws a red dot, right-clicking draws a yellow dot
# Press q or esc to move to next image
# Once an image is finished, a version with click locations overlaid is saved to file
# Numbers of left and right clicks are embedded into filename

allfiles=os.listdir(os.getcwd())
filelist=[f for f in allfiles if f[-4:] in ['.jpg','.JPG','.jpeg','.JPEG']]

dotfrac=0.0035

for imname in filelist:
    pygame.init()
    inf=pygame.display.Info()
    sw,sh=inf.current_w,inf.current_h

    PhotoSurface = pygame.image.load(imname)
    ow,oh=PhotoSurface.get_size()
    if ((float(ow)/float(oh))>(float(sw)/float(sh))):
        size=(sw,int(oh*float(sw)/float(ow)))
    else:
        size=(int(ow*float(sh)/float(oh)),sh)
    dotradius=int(round(dotfrac*min(size)))
    screen = pygame.display.set_mode(size,pygame.FULLSCREEN)
    PhotoSurface = pygame.transform.scale(PhotoSurface,size)
    background = pygame.Surface(size)

    screen.blit(PhotoSurface, (0, 0))
    pygame.display.flip()

    leftcoords,rightcoords=[],[]

    running=True
    while running == True:
        for event in pygame.event.get():
            if event.type ==KEYDOWN and event.key in (K_q,K_ESCAPE):
                running=False
            else:
                if event.type == MOUSEBUTTONDOWN:
                    mx,my=event.pos
                    if event.button==1:
                        leftcoords.append([mx,my])
                    if event.button==3:
                        rightcoords.append([mx,my])
                    screen.blit(PhotoSurface, (0, 0))
                    for coord in leftcoords:
                        pygame.draw.circle(screen, (255,0,0), coord, dotradius)
                    for coord in rightcoords:
                        pygame.draw.circle(screen, (255,255,0), coord, dotradius)                
                    pygame.display.flip()

    fname=imname[0:-4]+"_L%04d_R%04d.png"%(len(leftcoords),len(rightcoords))
    pygame.image.save(screen,fname)
    pygame.quit()
sys.exit(0)