Building cell models and simulations from microscope images

Abstract

The use of fluorescence microscopy has undergone a major revolution over the past twenty years, both with the development of dramatic new technologies and with the widespread adoption of image analysis and machine learning methods. Many open source software tools provide the ability to use these methods in a wide range of studies, and many molecular and cellular phenotypes can now be automatically distinguished. This article presents the next major challenge in microscopy automation, the creation of accurate models of cell organization directly from images, and reviews the progress that has been made towards this challenge.

OrNet - a Python Toolkit to Model the Diffuse Structure of Organelles as Social Networks

“…Thus, arises the need to find a methodology that generates quantitative models capable of accurately describing the data (Eliceiri KW, 2012). Prior works have demonstrated success in the generation of static models for subcellular modeling (Chen et al, 2018;Murphy, 2015;Ruan et al, 2019). Such advancements have inspired us to propose a novel framework, OrNet, that models both the spatial and temporal morphology changes that organelles undergo as dynamic social networks.…”

From observing to predicting single-cell structure and function with high-throughput/high-content microscopy

“…Generative models aim to generate (i.e. simulate) new typical examples of the data under study to investigate statistical variability, allow a more accurate and intuitive way to describe a particular localisation or enable better and more realistic cellular models [101]. For instance in an earlier study the authors were able to learn conditional generative models of punctuate patterns knowing microtubule localisation, enabling the study of relative positions of organelles with single-cell resolution [102].…”

When Deep Learning Meets Cell Image Synthesis

“…Finally, learning sizes or distributions of cell components have also been tried out for some object types like mitochondria but this research direction is still waiting for proper exploration.…”