STracking: a free and open-source Python library for particle tracking and analysis

Abstract

Summary Analysis of intra and extra cellular dynamic like vesicles transport involves particle tracking algorithms. The design of a particle tracking pipeline is a routine but tedious task. Therefore, particle dynamics analysis is often performed by combining several pieces of software (filtering, detection, tracking…) requiring many manual operations, and thus leading to poorly reproducible results. Given the new segmentation tools based on deep learning, modularity and interoperability between software have become essential in particle tracking algorithms. A good synergy between a particle detector and a tracker is of paramount importance. In addition, a user-friendly interface to control the quality of estimated trajectories is necessary. To address these issues, we developed STracking, a python library that allows combining algorithms into standardized particle tracking pipelines. Availability and Implementation STracking is available as a python library using “pip install” and the source code is publicly available on GitHub (https://github.com/sylvainprigent/stracking). A graphical interface is available using two napari plugins: napari-stracking and napari-tracks-reader. These napari plugins can be installed via the napari plugins menu or using “pip install”. The napari plugin source codes are available on GitHub (https://github.com/sylvainprigent/napari-tracks-reader, https://github.com/sylvainprigent/napari-stracking). Supplementary information Supplementary data are available at Bioinformatics online.

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“…Using the first frame of the obtained time lapse videos, the individual characteristics of the mitochondria were analyzed: area, mean TMRE fluorescence intensity, and eccentricity, which characterizes the degree of roundness of mitochondria ( Figure 9 A). To analyze the mPTP opening time, both the raw frames and the predicted mitochondrial segmentation masks were further processed using STracking (accessed on 31 January 2024) [ 64 ], an open-source library implemented in Python version 3.9 that allows the tracking of cellular compartments. The obtained data on the movement of mitochondria over time and changes in the brightness of their pixels were used for further analysis of the dynamics of mPTP opening ( Figure 9 B).…”

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