9 September 2016

MaCSBio/NUTRIM paper published in Bioinformatics

The paper 'Estimating real cell size distribution from cross-section microscopy imaging' by the Maastricht Centre for Systems Biology (MaCSBio) and the Department of Human Biology NUTRIM School of Nutrition and Translational Research in Metabolism has been published in Bioinformatics.

Motivation
Microscopy imaging is an essential tool for medical diagnosis and molecular biology. It is particularly useful for extracting information about disease states, tissue heterogeneity and cell specific parameters such as cell type or cell size from biological specimens. However, the information obtained from the images is likely to be subjected to sampling and observational bias with respect to the underlying cell size/type distributions.

Results
We present an algorithm, Estimate Tissue Cell Size/Type Distribution (EstiTiCS), for the adjustment of the underestimation of the number of small cells and the size of measured cells while accounting for the section thickness independent of the tissue type. We introduce the sources of bias under different tissue distributions and their effect on the measured values with simulation experiments. Furthermore, we demonstrate our method on histological sections of paraffin-embedded adipose tissue sample images from 57 people from a dietary intervention study. This data consists of measured cell size and its distribution over the dietary intervention period at four time points. Adjusting for the bias with EstiTiCS results in a closer fit to the true/expected adipocyte size distribution with earlier studies. Therefore, we conclude that our method is suitable as the final step in estimating the tissue wide cell type/size distribution from microscopy imaging pipeline.

Availability and Implementation
Source code and its documentation are available athttps://github.com/michaelLenz/EstiTiCS. The whole pipeline of our method is implemented in R and makes use of the ‘nloptr’ package. Adipose tissue data used for this study are available on request.

Associated organisations

Contact

Maastricht Centre for Systems Biology (MaCSBio)

The primary aim of the Maastricht Centre for Systems Biology (MaCSBio) is to facilitate the integration of biological data coming from several empirical domains using mathematical multi-scale modelling approaches. The centre is a joint initiative of the Faculty of Psychology & Neuroscience, Faculty of Health, Medicine & Life Sciences, and Faculty of Humanities and Sciences.

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School of Nutrition and Translational Research in Metabolism (NUTRIM)

NUTRIM School of Nutrition and Translational Research in Metabolism aims to contribute to excellence in health maintenance and personalized medicine by unraveling lifestyle and disease induced derangements in metabolism and by developing targeted nutritional, exercise and drug interventions. This is facilitated by a state of the art research infrastructure and close interaction between scientists, clinicians, master and PhD students.

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