Do they perform flow cytometry of bone marrow aspirate?
Flow cytometry can be performed on any group of cells, so yes, it can be performed on the bone marrow aspirates.
Does the ordering clinician specify which antibodies to use, or does s/he just specify which disease he's looking for, or does he specify nothing and leave it up to the hematopathologist?
Clinicians (in general) do not order flow cytometry on anything because it is not a test with which they are familiar. A clinician provides tissue to a pathologist for a suspected disease process. The pathologist then decides whether flow cytometry would be a valuable adjunct in the evaluation of any pathology. As with all consultations of a pathologist, a clinician should provide a complete HPI to the pathologist to aid in thorough evaluation and diagnosis.
How does one interpret the flow cytometry scatter plot?
Very carefully and only after much practice.
Which is more sensitive and specific, flow cytometry or microscopy? Is flow cytometry essentially a more sensitive and precise alternative to blood films?
Flow cytometry is a test like any other performed in a standard hospital laboratory (albeit a complicated and labor intensive test). It is used just like any other test, as an adjunct that can be invaluable in certain circumstances and misleading in others. Flow cytometry is used in conjunction with histologic findings for the purpose of diagnosis, but it will never replace standard microscopic histology in the same way that million dollar laboratory work-ups as soon as a patient walks into the ER will never replace a thorough H&P.
As an aside, you ask a lot of very general questions in a number of forums and would perhaps be better served by reading more generally about medicine and concentrating on wherever you are in the process of becoming a physician. Wait until at least the 2nd year of medical school before you start investigating the minutiae of every medical specialty.
