The Imaging facility of the Division has ample choice of Software at the disposal of the users.
NIH Image J
FCS Express 4 Image Cytometry
FCS Express 4 Flow Cytometry
In addition, the proprietary Aperio software for image analysis and handling are installed.
An example of quantitative image analysis of lymphoid populations in FFPE tissue sections is given at this link.
With this method, multiple cell types can be distinguished and quantified. As an example see at this link how five different lymphoid cell populations may be quantified by using a simple double IF on routinely fixed, embedded tissue.
A routine tonsil tissue is stained in triple IF (T cells, B cells and nuclei) and each individual lymphocyte is identified by phenotype and antigen density.