Immunohistochemistry (IHC) plays an essential role in Pathology. In order to improve reproducibility and standardization of the results interpretation, IHC quantification methods have been developed. IHC interpretation based in whole slide imaging or virtual microscopy is of special interest. The objective of this work is to review the different computer-based programs for automatic immunohistochemistry and Fluorescence In Situ Hybridization (FISH) evaluation. Scanning solutions and image analysis software in immunohistochemistry were studied, focusing especially on systems based in virtual slides. Integrated scanning and image analysis systems are available (Bacus TMAScore, Dako ACIS III, Genetix Ariol, Aperio Image Analysis, 3DHistech Mirax HistoQuant, Bioimagene Pathiam). Other image analysis software systems (Definiens TissueMap, SlidePath Tissue Image Analysis) can be applied to several virtual slide formats. Fluorescence is the preferred approach in HistoRx AQUA, since it allows for a better compartmentalization of signals. Multispectral imaging using CRi Nuance allows multiple antibodies immunohistochemistry, and different stain unmixing. Most current popular automated image analysis solutions are aimed to brightfield immunohistochemistry, but fluorescence and FISH solutions may become more important in the near future. Automated quantitative tissue microarrays (TMA) analysis is essential to provide high-throughput analysis. Medical informatics standards in images (DICOM) and workflow (IHE) under development will foster the use of image analysis in Pathology Departments.