Hi, I’m really new to imageJ/Fiji and I’m trying to process a batch of images of bacterial counts so that I can count them. Here are examples of my starting and processed photos:
Essentially I just want to adjust the brightness/contrast a bit so that when I tranform the image into a binary image it will make an image that isn’t noisy so I can count the number of cells accurately.
I made a macro from plugins>macro>record, and attempted to run this macro on all the images through process>batch>macro. Here is the macro I recorded:
run("8-bit"); //run("Brightness/Contrast..."); setMinAndMax(46, 199); run("Apply LUT"); run("Close"); setAutoThreshold("Default dark"); //run("Threshold..."); setOption("BlackBackground", false); run("Convert to Mask"); run("Close"); run("Analyze Particles...", "exclude summarize");
However, when I try to run this with a batch, I get an error message that either says “there are no images open” or (if I have all of the images I want to process open) it will say “A threshold image or 8-bit binary image is required”. This makes me very confused because they are supposed to be converted to an 8-bit image in the first step. If someone could explain how to write and run a macro that adjusts brightness/contrast, then converts to an inverted binary image for cell counts, that would be absolutely fantastic. Thanks!