The best is to take photos in microscope attached to computer as it has inbuilt software to add scale bars, and also the image clarity is better which is required for tissue culture publications.
But if you don't have that set-up, you can take pictures on any light microscope and simultaneously take pictures of ruler scale at different magnification (which are used for clicking photos).
Then using image J you can add scale bar, it's free software
Each and every stage and all the observations should be documented as photographs. find a good place for photography, it is an important step as it results depend on or are evidenced by the photos.
Adjust light sources to get good photos. Use a ruler while taking photos and finally you can draw scale bars according to the ruler sizes. If it is microscopic images, scale bars are available in the software itself.
Kokila Wickramanayake quality photographs are a must to publish your results in a journal. Select a perfect background color and source of light since the cultures are in glass jars or bottles only. If the cultures are of somatic embryos or micro shoots use a stereo microscope for better pictures. For scale bars follow Dr. Manokari's advice, this will help you practically.
Photography as a Tool of Research and Documentation in Plant Tissue Culture
An excellent paper, will help you out. Simple methods for improving the results of photography in plant tissue culture are discussed, along with photographic equipment, photomacrography, stereophotomicrography, suitable backgrounds for photography, use of a digital scanner, and the construction of photographic plates.