TopoCell - An image analysis tool to study intracellular topography

We aim to build an open source bioimage informatics tool capable of analyzing 2D and 3D topography (absolute and relative localization, shape, size and intensity) of distinct types of intracellular particles (such as organelles, proteins, lipids and other detectable biomolecules) in different types of cells in a high‐throughput fashion. To achieve this, TopoCell is primarily designed to run fluorescence microscope images, where all possible channels imaged are used to semi‐automatically detect different particles, define cell type and segment cells. To each detected particle, a coordinate, intensity, volume, and sphericity value are attributed. Cells are detected through a plasmalemma marker, where volume and coordinate values are generated after the segmentation step. Numerous cell types can be defined by the user accordingly to the density of given intracellular particles. By controlling a dedicated filter, the user can select which cells and particles to consider in the analysis according to their detected values, including relative distance between two or more types of particles. Visualization of results and statistical analysis are also available. TopoCell allows us to comprehensively measure in still microscope images, the distribution of intracellular phenomena which otherwise would be negligible to the naked eye, as for instance translocation or particle association.