ImageJ 
ImageJ is a free softwarebased on JAVA language, developed by the NIH and broadly used by the scientific community. Numerous plugins and macros are available and allow to perform custom operations.
Application examples
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Nuclear counting
Endothelial cells - caveolin/Connexin/DAPI IF
.zvi image acquired in structured illumination (AxioImager.z1/ApoTome) - x40 objective
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Analysis of fluorescence staining intensity
Cardiomyocytes - OGT/alpha-sr-actinin/DAPI IF
.zvi image acquired in structured illumination (AxioImager.z1/ApoTome) - x63 objective
Red area quantification above a threshold (within cell, nucleus, cytoplasm)
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Analysis of the distance between lysosomes and nucleus
Tumor cells - LAMP1/WGA/DAPI IF
.zvi image acquired by structured illumination (AxioImager.z1/ApoTome) - x40 objective
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Assembly of a mosaic of overlapping individual images (MosaicJ plugin)
Reconstitution of a section of mouse heart (Rhodamin-WGA staining) from images acquired in epifluorescence (AxioImager.z1)
Useful plugins and macros:
LOCI Tools (opening of several image formats)
Cell counter (manual counting of several cell types)
Angiogenesis analyzer (analysis of cellular networks)