I have done a fluorescent IHC-P for Iba-1, and tried to double stain it with CD16/32 (the second Ab seems to failed). Iba-1 is a good staining but too general.
If your sure the absence of CD16/32 is not because of any issues due to fixation-sensitivity or primary antibody concentration I would try CD68, MHC-II or CD45. Each of these have very low constitutive expression but can be dramatically up-regulated with injury. Note that expression of each of these on microglia can increase with injury but if there is any probability of a BBB compromise then infiltration monocytes could be driving the enhancement of signal.
Also it may be worth looking at an interesting paper:
Novel objective classification of reactive microglia following hypoglossal axotomy using hierarchical cluster analysis
Jun Yamada andShozo Jinno*
Article first published online: 29 JAN 2013
Also I have just put out a review on the relationship between morphology an activation states - but I'm sure your after protein based markers of activation state.
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