Coloring what for?

Photoshop.

I do not love these colorful pictures, but if you really want, you can also use Digital Micrograph, for example with:

http://www.dmscripting.com/applyclut.html

Actually I hate seeing colored micrographs in publications.

But I do like coloring pictures 

https://www.researchgate.net/publication/243373092_Coloring_Pictures_for_Electron_Microscopists_or_Elements_of_Digital_Image_Manipulation_for_Students

Article Coloring Pictures for Electron Microscopists, or Elements of...

@Vladimir: Nice examples in your paper. But easier to use is the following link: ;-)

http://journals.cambridge.org/action/displayFulltext?type=1&fid=1944048&jid=MAM&volumeId=14&issueId=S2&aid=1944044&bodyId=&membershipNumber=&societyETOCSession=

Thanks Vlaidmir and volker klemm for your suggestion. I am not getting the way to colour images using DM. I tried with photoshop and that has made me to colour them beautiful. 

I would suggest you to use ITEM software to get the colorful image.

i don't know its free of cost or not but certainly you can search it .

Thank you Praveen. but i will be pleased if you can upoad the link for that, since the name of the software seem like item so i am not getting the one software which you are talking about. 

http://www.soft-imaging.net/en/eu/eng/2343_5894.htm

Thanks Praveen, I will try to get that software.