Author: Agnese Callegari

Video microscopy has a long history of providing insights and breakthroughs for a broad range of disciplines, from physics to biology. Image analysis to extract quantitative information from video microscopy data has traditionally relied on algorithmic approaches, which are often difficult to implement, time consuming, and computationally expensive. Recently, alternative data-driven approaches using deep learning have greatly improved quantitative digital microscopy, potentially offering automatized, accurate, and fast image analysis. However, the combination of deep learning and video microscopy remains underutilized primarily due to the steep learning curve involved in developing custom deep-learning solutions. To overcome this issue, we have introduced a software, currently at version DeepTrack 2.1, to design, train and validate deep-learning solutions for digital microscopy.

Video microscopy has a long history of providing insights and breakthroughs for a broad range of disciplines, from physics to biology. Image analysis to extract quantitative information from video microscopy data has traditionally relied on algorithmic approaches, which are often difficult to implement, time consuming, and computationally expensive. Recently, alternative data-driven approaches using deep learning have greatly improved quantitative digital microscopy, potentially offering automatized, accurate, and fast image analysis. However, the combination of deep learning and video microscopy remains underutilized primarily due to the steep learning curve involved in developing custom deep-learning solutions.

To overcome this issue, we have introduced a software, currently at version DeepTrack 2.1, to design, train and validate deep-learning solutions for digital microscopy. We use it to exemplify how deep learning can be employed for a broad range of applications, from particle localization, tracking and characterization to cell counting and classification. Thanks to its user-friendly graphical interface, DeepTrack 2.1 can be easily customized for user-specific applications, and, thanks to its open-source object-oriented programming, it can be easily expanded to add features and functionalities, potentially introducing deep-learning-enhanced video microscopy to a far wider audience.

Deviations from the law of Brownian motion, typically referred to as anomalous diffusion, are ubiquitous in science and associated with non-equilibrium phenomena, flows of energy and information, and transport in living systems. In the last years, the booming of machine learning has boosted the development of new methods to detect and characterize anomalous diffusion from individual trajectories, going beyond classical calculations based on the mean squared displacement. We thus designed the AnDi challenge, an open community effort to objectively assess the performance of conventional and novel methods. We developed a python library for generating simulated datasets according to the most popular theoretical models of diffusion. We evaluated 16 methods over 3 different tasks and 3 different dimensions, involving anomalous exponent inference, model classification, and trajectory segmentation. Our analysis provides the first assessment of methods for anomalous diffusion in a variety of realistic conditions of trajectory length and noise. Furthermore, we compared the prediction provided by these methods for several experimental datasets. The results of this study further highlight the role that anomalous diffusion has in defining the biological function while revealing insight into the current state of the field and providing a benchmark for future developers.