Bivariate spatial point patterns in the retina: a reproducible review

Eglen, Stephen J.

Journal de la société française de statistique, Tome 157 (2016) no. 1, pp. 33-48.

Cette revue présente des résultats récents sur la position de neurones de différents types tout en mettant en application les principes de la « recherche reproductible ». Une attention particulière est portée aux positions relatives de différents types cellulaires de la rétine. Trois hypothèses explicatives de l’agencement de deux types de neurones sont considérées : les cellules des différents types sont positionnées indépendamment les unes des autres ; les cellules d’un seul type se voient affectées aléatoirement deux labels différents créant ainsi deux populations liées ; des interactions entre les cellules de différents types génèrent les dépendances spatiales. L’application des techniques de statistique spatiale à l’étude de ces trois hypothèses est brièvement exposée. Ce travail est de surcroît un exemple de « recherche reproductible »car l’ensemble des programmes (informatiques) ainsi que l’ensemble des données sont intégrés au manuscrit ce qui permet à tout lecteur de reproduire l’analyse proposée. La revue se conclut par une discussion du concept de « recherche reproductible ».

In this article I present a reproducible review of recent research to investigate the spatial positioning of neurons in the nervous system. In particular, I focus on the relative spatial positioning of pairs of cell types within the retina. I examine three different cases by which two types of neurons might be arranged relative to each other. (1) Cells of different type might be effectively independent of each other. (2) Cells of one type are randomly assigned one of two labels to create two related populations. (3) Interactions between cells of different type generate functional dependencies. I show briefly how spatial statistic techniques can be applied to investigate the nature of spatial interactions between two cell types. Finally, I have termed this article a ‘reproducible review’ because all the data and computer code are integrated into the manuscript so that others can repeat the analysis presented here. I close the review with a discussion of this concept.

Keywords: retinal mosaics, spatial statistics, reproducible research, mathematical modelling, computational neuroscience
Mot clés : mosaïque rétinienne, statistique spatiale, recherche reproductible, modélisation mathématique, neurosciences computationnelles

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