We use well established stereological tools to obtain unbiased estimates of cellular features like sizes, volumes or numbers of organelles and particles. In an initial step a rigorous sampling scheme ensures unbiased selection of the areas/locations of interest. In most cases this sampling scheme is carried out by a systematic uniform random placement throughout the specimen which gives every location an equal chance of being included in the sample. In a second step we apply stereological estimators in form of geometrical probes onto the sampled micrographs/locations and count “events” between those probes and the underlying ultrastructural features. Depending on the desired parameter these probes can be points, lines or planes. An example would be the estimation of the area of an organelle by point counting. A regular array of equally spaced points is used to count points that land over the areas of interest. The number of points multiplied by the area associated with one of those points on the grid lattice will be an estimate of profile area of that organelle.

For 3D quantitation we analyse consecutive serial sections to obtain data about organelle volumes and number.

Useful links:


J. Lucocq & C. Hacker. Cutting a fine figure - on the use of thin sections in electron microscopy to quantify autophagy. 2013. Autophagy

J. Lucocq, T. Mayhew, Y. Schwab, A. Steyer and C. Hacker. Systems biology in 3D space - enter the morphome. 2015. Trends in Cell Biol.

S. Tschanz, J. Scheider and L. Knudsen. Design-based stereology: Planning, volumentry and sampling are crucial steps for a successful study. 2014. Annals of Anatomy.

R. Marcos, R. Monteiro and E. Rocha. The use of design-based stereology to evaluate volumes and numbers in the liver: a review with practical guidelines. 2012. Journal of Anatomy.

Estimation of area using point counting

Estimation of area using point counting