Suggest two or three possible disadvantages in using staining in microscopic preparations.?

- Staining can kill specimens, so can't stain if you want live specimens
- Not all stains work on all specimens, with some retaining it and others not

A few:

Staining requires extra training and expertise to work properly, and you need to have some idea as to what you are looking for to choose the right stain. This can make it a more complicated task and you can miss things if you don't use the specific stain you need to show up whatever it is you're looking for.

Staining is also usually pretty permanent and limit what else you can do with the sample- once it's stained and prepared there's usually not much else you can do with it except look at it under the microscope with that stain.

On the other hand, stains reveal so much information if used correctly that's its usually worth it by a long shot.

One example of where these come into play is with biopsy material of, say, cancer. Usually there's only so much material available so the pathologist has to know what stain to use to analyse it. On the other hand, they will usually know why the biopsy was taken and what they're looking for, so this is obviously helpful in that regard.

o You spilled some and it made a big mess.
o You got some on your hands, you can't wash it off, and your lab teaching assistant is going to give you a bad mark for not wearing gloves.
o Your girlfriend won't go out with you until that stain has completely worn off your hands.

o You're trying to look at activity inside a living cell. The stain has kind of gummed up all sorts of things inside and on the membrane of the cell, so the cell is somewhere between "sick" and "dying." You're not going to be observing normal behavior.
o The more involved your staining procedure is, the more likely that you will be making "artifacts" -- things that are visible that are the result of the staining procedures and aren't anything that came from your sample, or your preparing methods have gotten things stuck together into unrecognizability.
o Stains cost money.
o If you heat-fixed your specimen onto the slide, you can't wash off the slide and reuse it, because some of that stuff is going to remain behind and would be artifacts for the next use of the slide. Slides cost money.

Yeah. You should check out lighting tricks such as phase-contrast, which don't involve poisoning and artifacting your specimen.