Histology imaging:
– TMARKER: standalone cell nuclei counting and staining aid (JAVA based)
– ImmuneRatio web-based analyses / also plugin for IJ (html)

Superresolution imaging software collection:
– EPFL collection

Cell Cycle analysis:
– CellCognition Project – time lapse analyses of the cell cycle

 AFM freeware: 
– GWYDDION