AMCB: A software toolkit for construction and analysis of Aggregate Maps in Cell Biology

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Nuclear biology is concerned with understanding the construction and operation of the cell nucleus, a major component of mammalian cells, which carries the bulk of the genetic material and regulates many aspects of cellular operation.The cell nucleus is an incredibly complex entity which undergo dynamic changes throughout the cell's lifecycle. Research in cell biology is crucial to fully understand the basic operation of this fundamental unit of life. In turn, this understanding translates into insight about a host of diseases, and the distant promise of diagnostic markers and even cures. In addition to genetic material, the nucleus contains a great deal of other molecular machinery that is crucial for normal operation. Examining suitably prepared microscopy images of the nucleus reveals a complex arrangement of functional objects that instantiate this machinery. These objects, often punctate, appear to scatter randomly inside nucleus. However, close inspection of multiple nuclei and quantitative analysis suggest that the scattering of these objects, while stochastic, appears to follow subtle rules. These observations provide that tantalising suggestion that the spatial layout of the components of the nucleus are, in part, positioned in a manner that reflects their functional roles. However, existing analysis tools are typically based on a relative assessment of spatial preference. For example, functional objects of one type are observed in close proximity to functional objects of a different type. Such analysis is adequate for making statements about the relationship between the specific functional objects, but provides no information about the absolute spatial preference of the objects within the nucleus. This research will provide new data analysis methodology that will explicitly address this shortcoming. The fundamental hypothesis is that there is some absolute spatial organisation that can be captured by examining multiple nuclear images in a novel way. This novel approach consists of a collection of mathematical transformations from the area of statistical shape analysis. These transformations first find the average shape of the nucleus from multiple images, and then use a special mathematical deformation to force each nucleus and it interior into the average shape. In this way, all nuclei are placed in a common coordinate system, which means analysis of absolute spatial preference is possible. The collection of data in the common coordinate system is called an aggregate map (AM). Analysis and visualisation of the AM provides completely new insights about spatial architecture, and offers great opportunities for analysis of perturbed cells. A number of research steps are required to develop this methodology for analysis of 3-dimensional confocal microscopy images, including a very thorough evaluation phase. On completion of this research, we will release AMCB, a software tool for constructing and analysing aggregate maps. This will allow cell biology researchers worldwide to move towards the ultimate end point of a fully functioning model of a virtual cell nucleus and to uncover the basic principles underlying its functional organisation.