First of all I would like to thank the great effort you are doing. I really appreciate it.
Second, I would like to ask if you can help me with a couple of issues:
I am trying to count the number of yeast colonies on agar plates. I have set up a device where I illuminate the plates from underneath in a dark room, and where the camera and the plates are always in the same position. That gives me a light background, so I have included a module to invert the color of the plate. I have adjusted the parameters of the pipeline ExampleYeastColonies_BT_PIPE.mat so that it does a pretty good job in counting the colonies (pipeline attached: ContarColoniasFondoBlancoPIPE.mat). The problems starts here:
The plasticware has a plastic rim underneath the plate that shows on the photos like an inner rim, and the program counts its pixels like colonies (see SANY0070_outlines.png). I cannot get rid of the plastic rim, so I thought of subtracting it: I took a photo of an empty plate (SANY0075.JPG), colored in red the inner rim (PlateTemplateRed.png) and tried to subtract it. And that’s where I got stuck. I’ve tried so many different combinations that I’ve lost track, and I don’t know what I am doing wrong. I think I should first align the images, but I get an error that it should be black and white. Nevertheless it tells me that it’s going to convert my image to B&N and then use the correction to align the color image. Then I’ve tried to subtract the red from the red original image (CropRedPlate), but I get the program to count even more accurately the pixels of the rim. So, I’ve tried adding it, with the same result!!!. I’ve converted the image with the red rim into an image with the rim in green and blue (PlateTemplateNORed.png), in an attempt to subtract or to add to the CropCombined, with no luck…I know I MUST be making some mistake, because my logic and the little I have managed to learn of the program tells me that it can be done this way, but I give up and I want to ask if you can give me a little push.
The other issue, very minor, is that I only need the program to count for me the number of colonies, I do not need all the additional information, and I’ve looked arround to see if I could remove the rest, but with not much success. It’s not too important, so if it gets complicated or are very busy, ignore this one, but if its not a big effort, then the program would be absolutely perfect for my needs!
I attach a couple of plates. You will observe that the colonies I have vary extremely in size (from 1 to 20 pixels), because of the treatment. I know it’s not the prefered format, but the cammera takes JPG pictures, so that’s what I send you. If you’d rather me converting them, tell me and I’ll do it!
ContarColoniasFondoBlancoPIPE.mat (2.67 KB)ContarColoniasFondoBlancoPIPE.mat (2.67 KB)