Lightweight and Scalable Particle Tracking and Motion Clustering of 3D Cell Trajectories Tracking cell particles in 3D microscopy videos is a challenging task but is of great significance for modeling the motion of cells. Proper characterization of the cellu0027s shape, evolution, and their movement over time is crucial to understanding and modeling the mechanobiology of cell migration in many diseases. One in particular, toxoplasmosis is the disease caused by the parasite Toxoplasma gondii. Roughly, onethird of the worldu0027s population tests positive for T. gondii. Its virulence is linked to its lytic cycle, predicated on its motility and ability to enter and exit nucleated cells; therefore, studies elucidating its motility patterns are critical to the eventual development of therapeutic strategies. Here, we present a computational framework for fast and scalable detection, tracking, and identification of T. gondii motion phenotypes in 3D videos, in a completely unsupervised fashion. Our pipeline consists of several different modules including preprocessing, sparsification, cell detection, cell tracking, trajectories extraction, parametrization of the trajectories; and finally, a clustering step. Additionally, we identified the computational bottlenecks, and developed a lightweight and highly scalable pipeline through a combination of task distribution and parallelism. Our results prove both the accuracy and performance of our method.

A TwoTier Convolutional Neural Network for Combined Detection and Segmentation in Biological Imagery Deep learning techniques have been useful for modern microscopy imaging techniques to further study and analyze biological structures and organs. Convolutional neural networks (CNN) have improved 2D object detection, localization, and segmentation. For imagery containing biological structures with depth, it is especially desirable to perform these tasks in 3D. Traditionally, performing these tasks simultaneously in 3D has proven to be computationally expensive. Currently available methodologies thus largely work to segment 3D objects from 2D images (without context from captured 3D volumes). In this work, we present a novel approach to perform fast and accurate localization, detection, and segmentation of volumes containing cells. Specifically, in our method, we modify and tune two stateoftheart CNNs, namely 2D YOLOv2 and 3D UNet, and combine them with a new fusion and image processing algorithms. Annotated volumes in this space are limited, and we have created synthetic data that mimics actual structures for training and testing our proposed approach. Promising results on this test data demonstrate the value of the technique and offers a methodology for 3D cell analysis in real microscopy imagery.