knee and thigh strengthening exercises

If you have significant atrophy like you mentioned, it may be a good idea to work with a PT to help build up your muscle strength and muscle mass. This will require some time in order for you to get to where you at prior to your injury. For my patients who have sustained similar injuries as yourself, beginning exercises which I would have them perform to help with quadriceps strengthening can include quad sets, straight leg raises, short arch quads and long arch quads. I can than progress my patients by utilizing ankle weights. Once they are cleared for weight bearing, I can incorporate partial squats, lunges, the use of machines, etc. to their exercise program. There will probably be other issues going on such as strength and range of motion deficits at other areas as well ie. hip, ankle that needs to be addressed as a result of the immobility. Careful and appropriate progression of exercise will be an important component of rehab so like I mentioned previously, it may be a good idea to work with a physical therapist if you can.