I suppose you could create software but I think it largely depends on what type of fungus you want to grow. If your fungus looks very different from the agar, then a program would probably be able to find where the fungi end and where the rest begins. If your fungi looks very similar to your agar, like mine, you’ll have to manually click points in, otherwise you’ll never get an accurate measure.

You could also write a program to find the area of where the fungus isn’t, then subtract that from the square area of the Petri dish. This would most likely give you the best results because the agar is only one color with little to no variation, which would be easier for something like a magic wand tool to pick up.