Michael-shannon/cellPLATO: cellPLATO

This is the 2023 version of cellPLATO (cell Plasticity Analysis Tool) developed in collaboration with @tsloan1377 @Quorumetrix. CellPLATO is a semi-automated morpho-kinetic analysis tool for cell tracking data.

It takes cell tracking data as an input, makes motility, morphology and clustering measurements for each cell at each timepoint, then outputs statistical plots of difference and plots of difference over time in python (inspired by those developed in R by @JoachimGoedhart ).

Then, dimensionality reduction and cluster analysis are used to separate cells into behavioural subsets based on combinations of these morpho-kinetic measurements, producing a fingerprint of behaviour types per biological condition: how many of the cells operate behaviour a versus behaviour b or behaviour c, and over what timescale?

Finally, the disambiguation step automatically picks cells most representative of a given behaviour in dimensionally reduced space, extracts them along with the metrics that best define them, and displays them as figures in 'human space', enabling humans to understand the shape and motion characteristics defined by the software in each behaviour case.