Wednesday 16 March 2016

One-Stop Stereology: the estimation of 3D parameters using Isotropic Rulers (2009)

I have pretty much given up writing scientific research papers. Much as I enjoyed it whilst I was doing it, the nitpicking and finalizing required to get a paper accepted and published has worn me out. I would now rather try and write books.

The paper below, One-Stop Stereology: the estimation of 3D parameters using Isotropic Rulers, was published in 2009 in the Journal of Microscopy. The paper was the culmination of about 5 or 6 years of trying really hard to simplify the concepts around and data collection for estimating statistical functions of the 3D structure of microscopic anatomical features. A field known as second-order stereology.


The stereological estimation of second-order descriptors of spatial architecture appears to be inherently more time-consuming and labour-intensive than the estimation of first-order quantities (total quantities or ratios). Therefore, far fewer researchers tend to make use of second-order approaches in their stereological research projects. In this paper, we use a tutorial approach to illustrate how a desire for practical simplicity has provided us with a data collection method that can be used to simultaneously estimate both first-order and second-order properties of the microstructure of a defined anatomical feature of an organ. The approach does not rely on new results from theory, but nevertheless allows either isotropic uniform random or vertical uniform random sections to be used to make estimates of a comprehensive list of 10 microstructural parameters using relationships that are well known in the literature. The probe used in all cases is an isotropically distributed Ruler and the data collection protocol is easy to learn and apply. We illustrate the method on brain tissue but emphasize that the approach can also be applied to non-biological material.


The Journal of Microscopy was a great journal to publish in.  It was inherently multi-disciplinary and was interested in high quality papers and high quality production values. The font used was very clear - José Mendoza y Almeida's Photina (issued by Monotype for Photo composition in 1972. Bringhurst says of it, "one of the first and one of the finest postmodern text faces.").

As a microscopy journal, it always understood the high value of incorporating colour micrographs and was able to incorporate them and produce them at high quality. 

Below are a couple of two page spreads from the One-Stop Stereology paper. The full paper is HERE