If you need real time Mn concentration use Special dyes that bind to Mn and can be assayed in fluorometer / fluorescent microscope. You can consult Molecular Probes (invitrogen.com) for it
If ypou want to quantify in in microscopic structures you can use both TEM and SEM electron microscopy with x-ray fluorescence set-up. You will get a spectrum of all metal concentrations in small specific structures but with a high lower limit of etection. Good for accumulated trace elements concentrations. For a very high sensitivity bulk analyses use the carbon-rod atomic-absorption spectrometry with a detection limit of part per billion of the specific element of interest
Dear Raphael, Thank you for your input. Might you have more info on the microscopy methods or a paper reference? The high resolution provided by TEM would be ideal if it is sensitive enough. We are likely looking for micro molar Mn2+ above background. Warm regards, John