Nissl-stained sections segmentation using algorithms of Mathematical Morphology

The main part of presented algorithm is sequential homotopic thinning transformation, “invented” by a group of mathematicians, including F. Meyer (1976), Ch. Lantuejoul (1978), and headed by J.Serra, from Center for Mathematical Morphology, Fontainebleau, France. Many transformations based on thinning were described and published, including “SKIZ”, watersheds by flooding, and markers-controlled watersheds.

I personally learned about MM from “Summer School in Mathematical Morphology” (Fontainebleau, June 1981), and was very fortunate to be able to show some of these results to Professor Serra in 1983, when he was in Moscow and visited our Lab (see below). He was very happy to see how his ideas were implemented for the study of human brain. As far as I know, it was the first implementation of fully automated image processing technology for microscopy images of human cortex.

This picture was taken in Moscow, in 1983, during small reception after seminar with Prof. Serra in the Moscow Institute of Brain. Left to right: Prof V.M. Gindilis, Prof. J.P.Serra, Dr. V. Istomin

Practical results of the application of the algorithm presented below were published for the first time in 1984 (V. Istomin, M. Shkliarov, “Automatic analysis of cerebral cortex using television image analyzer”, Korsakov’s Bull. of Neuropathology and Psychiatry, v.7, pp.969-974), and in 1987 in USSR (Istomin, VV. Automatic morphocorticography of human brain (Technology development and application results). Dissertation of the Candidate of Medical Sciences.  (Автоматическая морфокортикография мозга человека (Разработка и результаты применения метода). Диссертация на соискание учёной степени кандидата медининских наук.), P.Lumumba’s University of Friendship of the Nations, Moscow, 1987.). Later it was published in 1990 in Europe (V. Istomin, K. Fiedler. Die Automatische Morphocorticographie – eine method zum Erfasses von Veranderungen der Zytoarchitektonik des menschlichen Cortex Cerebri. Bild und Ton, Jan, 1990, 11-14).

As one can imagine,  compared to present time, “the state of the art” of microscopy image processing was quite different thirty-plus years ago  One of many problems we had to face was extremely slow performance of digital skeleton algorithm. So, it had to be replaced for practical application by segmentation based on mean gradient distribution. Obviously, presented re-implementation of the segmentation is developed using quite different language and more powerful library (MAMBA-Image, CMM, see below), not to mention much faster and more powerful computer :-).

One thought on “Nissl-stained sections segmentation using algorithms of Mathematical Morphology”

Leave a Reply

This site uses Akismet to reduce spam. Learn how your comment data is processed.