To detect apoptotic nature of cells, make the cells stable with gfp or any other tag available to you and then follow the cells after implantation in vivo.
To check the apoptosis or necrosis on tissue fixed on the slides, do immunohistochemistry (IHC) of the specific marker proteins for apoptosis or necrosis.
You can easily search for the marker proteins on internet.
I wouldn't recommend annexin V conjugates, as they won't be able to intercalate into tissue well, nor are good for fixed and permed samples.
Instead, I recommend usage of fixation and then an anti-caspase antibody for IHC. Or you could use a TUNEL kit. APO-BrdU TUNEL kits will work, which use a BrdU derivative and an anti-BrdU antibody, but I instead recommend use of the Click-iT TUNEL kits, which don't have the drawbacks of antibody labeling.
I have a related question to the TUNEL assay, what can be used as a control sample. I want to perform this on fixed embedded and sectioned skeletal muscle tissue and I'm now wondering what could be a good way to have a control sample with a lot of apoptotic cells. Could a DNAse treatment after fixation still work?