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Prog Histochem Cytochem. 2013 Jan;47(4):211-333. doi: 10.1016/j.proghi.2012.09.001. Epub 2012 Nov 10.

Image cytometry: protocols for 2D and 3D quantification in microscopic images.

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Center for Applied Biomedical Research, S. Orsola-Malpighi University Hospital, Via Massarenti 9, I-40138 Bologna, Italy.


Microscopy-based imaging is booming and the need for tools to retrieve quantitative data from images is urgent. This book provides simple but reliable tools to generate valid quantitative gene expression data, at the mRNA, protein and activity level, from microscopic images in relation to structures in cells, tissues and organs in 2D and 3D. Volumes, areas, lengths and numbers of cells and tissues can be calculated and related to these gene expression data while preserving the 2D and 3D morphology. Image cytometry thus provides a comprehensive toolkit to study molecular processes and structural changes at the level of cells and tissues.

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