I have used FAA fixative (10% Formalin, 5% Acetic Acid, 50% Ethanol) to fix tomato apices for in situ but after fixation and 30 min vacuum infiltration the tissue becomes red-brownish. Do you know what could be the reason for it?
Ethanol concentration may be very high (50%). You can minimize ethanol concentration
30 min is long for the vacuum infiltration, this could damage the plant tissue. A few minutes should be sufficient.
You need to try high concentration low period of 5 minutes.
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