Hi,

you can use imageJ software. Convert your file into black and white picture, then you can make the software automaticaly count all spots (cells), then set a threshod in order to get only positive cells on the picture, count again and calculate the ratio positive/total. By keeping the threshold settings unchanged between pictures you should be able to treat all your datas without any bias. 

Thanks Guillaume - I will try this!

When converting to black and white - is there a specific file type (8-bit, 16-bit, jpg, tiff) that should be maintained? Also - do you know of any helpful tutorials that go through threshold setting and cell counting? 

Thanks again - I really appreciate your help!

You can convert to black and white in ImageJ.

There are some really good tutorials for ImageJ on Youtube actually. If you search for ImageJ and specifically what you want to do you can find whole protocols or sectional information. 

Thanks Cara - I will search for YouTube tutorials!