you can use  Olysia software. But it's not free. 

also you can find some good suggestions here: 

https://www.researchgate.net/post/What_is_a_good_program_software_for_Quantitative_Image_Analysis

You may want to try some free software such as Image J. It's very good for particles, but I can't say whether it's ideal for your application.

Hope it helps.

Hi, do you have downstream applications - or do you just need the counts? In case yiu do not need the slids afterwards: I would stain the spores to enhance the contrast (Lacto-glycerine cotton blue), take microscopic photos or a simple scan (depending on objects size) and than try Fiji (ImageJ), using thresholding and automatic counting (depending on quantity). It is useless, if the spores lie too close to each other and do not seperate in the picture. In some cases you need expensive software or a lot of patience -