The study, recently published in Biophysics Reviews, shows how artificial intelligence can be used to develop faster, cheaper and more reliable information about cells, while also eliminating the disadvantages from using chemicals in the process.
Countless systems in biology, physics, and finance undergo diffusive dynamics. Many of these systems, including biomolecules inside cells, active matter systems and foraging animals, exhibit anomalous dynamics where the growth of the mean squared displacement with time follows a power law with an exponent that deviates from 1. When studying time series recording the evolution of these systems, it is crucial to precisely measure the anomalous exponent and confidently identify the mechanisms responsible for anomalous diffusion. These tasks can be overwhelmingly difficult when only few short trajectories are available, a situation that is common in the study of non-equilibrium and living systems. Here, we present a data-driven method to analyze single anomalous diffusion trajectories employing recurrent neural networks, which we name RANDI. We show that our method can successfully infer the anomalous exponent, identify the type of anomalous diffusion process, and segment the trajectories of systems switching between different behaviors. We benchmark our performance against the state-of-the art techniques for the study of single short trajectories that participated in the Anomalous Diffusion (AnDi) challenge. Our method proved to be the most versatile method, being the only one to consistently rank in the top 3 for all tasks proposed in the AnDi challenge.
DeepTrack 2.0 Logo. (Image from DeepTrack 2.0 Project)Quantitative Digital Microscopy with Deep Learning Giovanni Volpe
Invited Talk at the Virtual school “Machine Learning and Automated Experiment in Scanning Probe Microscopy”
Online
October 4-7, 2021
11:20 AM
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 introduce a software, DeepTrack 2.0, 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 2.0 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.
Thomas Suphona defended his Master thesis in Physics at the Chalmers University of Technology on 27 september 2021. Congrats!
(Image from a composition of screenshots during Thomas Suphona’s Master Thesis defense)Title: Collective behaviors of autonomous robots in complex environment
Collective behaviours or collective motion is a common phenomena in nature where multiple organisms in a system undergo ordered movements. This can be observed in different scales, from the microscale with bacteria swarming to the macro scale with for example flocks of birds, schools of fish and even human crowds and car traffic.
All these systems are made up by self-propelling agents who are able to take up energy from their environment and converting it to directed motion.
Because of this
property of self-propulsion, their dynamics cannot be explained using conventional methods. Although significant efforts have been made in trying to explain collective behaviours from different perspective, using simulation tools and study systems in different scales as mentioned before, the subject is not as widely studied from the macroscale, especially with artificially made systems. In this thesis, a macroscale system was design with the purpose of providing conditions for collective behaviours to emerge and study how the behaviours changes depending on the surrounding conditions. Battery powered robots were used as self-propelling agents and they were placed in a confined space filled with obstacles. It was shown that when the number of robot and obstacles inside the system is large, the robots movements were significantly restricted. The weight of the obstacles do also affect the average motions of the robots where heavier obstacles hinders the robots by creating blockage leading to the robots having lower average velocity. At certain configuration of the parameters, the robots showed collective behaviours where they for example form channels between the obstacles, making ”roads” for other robots to reuse, or helping each other to move by pushing away chunks of obstacles or pushing onto each other. Even though these robots are simple agents, they have manage to manifest cooperative actions towards other agents.
Supervisor: Giovanni Volpe and Alessandro Magazzú Examiner: Giovanni Volpe Opponent: David Fitzek
Aykut Argun starts his postdoc at the Physics Department of the University of Gothenburg on 21st September 2021.
Aykut has a PhD degree in Physics from the University of Gothenburg, Sweden.
During his postdoc, Aykut will continue his work on analysing stochastic trajectories with machine learning as well as experimental active matter systems.
Neural net with input layer (left), dense internal layers, and output layer (right). (Image from the article Machine Learning for Active Matter)Machine Learning for Active Matter: Opportunities and Challenges
Giovanni Volpe
Invited Talk
(online at) ICTP, Trieste, Italy
8 September 2021, 11:30 CEST
Machine-learning methods are starting to shape active-matter research. Which new trends will this start? Which new groundbreaking insight and applications can we expect? More fundamentally, what can this contribute to our understanding of active matter? Can this help us to identify unifying principles and systematise active matter? This presentation addresses some of these questions with some concrete examples, exploring how machine learning is steering active matter towards new directions, offering unprecedented opportunities and posing practical and fundamental challenges. I will illustrate some most successful recent applications of machine learning to active matter with a slight bias towards work done in my research group: enhancing data acquisition and analysis; providing new data-driven models; improving navigation and search strategies; offering insight into the emergent dynamics of active matter in crowded and complex environments. I will discuss the opportunities and challenges that are emerging: implementing feedback control; uncovering underlying principles to systematise active matter; understanding the behaviour, organisation and evolution of biological active matter; realising active matter with embodied intelligence. Finally, I will highlight how active matter and machine learning can work together for mutual benefit.
Barbora Spackova joins the Soft Matter Lab at the Physics Department of the University of Gothenburg on 1st September 2021.
Barbora has a PhD in physical engineering from the Czech Technical University in Prague (Czech Republic). Formerly, she has been a researcher at Chalmers University of Technology in the group of Prof. Christoph Langhammer. Her research is focused on single-molecule detection in nanofluidic systems.
While part of the Soft Matter Lab, she will continue her research on characterising cell media containing exosomes using Nanofluidic Scattering Microscopy (NSM).
M. xanthus cell-cell and cell-particle local interactions during cellular aggregation.The environment topography alters the transition from single-cell populations to multicellular structures in Myxococcus xanthus
Karla C. Hernández Ramos, Edna Rodríguez-Sánchez, Juan Antonio Arias del Angel, Alejandro V. Arzola, Mariana Benítez, Ana E. Escalante, Alessio Franci, Giovanni Volpe, Natsuko Rivera-Yoshida
Sci. Adv. 7(35), eabh2278 (2021)
bioRxiv: 10.1101/2021.01.27.428527
doi: 10.1126/sciadv.abh2278
The social soil-dwelling bacteria Myxococcus xanthus can form multicellular structures, known as fruiting bodies. Experiments in homogeneous environments have shown that this process is affected by the physico-chemical properties of the substrate, but they have largely neglected the role of complex topographies. We experimentally demonstrate that the topography alters single-cell motility and multicellular organization in M. xanthus. In topographies realized by randomly placing silica particles over agar plates, we observe that the cells’ interaction with particles drastically modifies the dynamics of cellular aggregation, leading to changes in the number, size and shape of the fruiting bodies, and even to arresting their formation in certain conditions. We further explore this type of cell-particle interaction in a minimal computational model. These results provide fundamental insights into how the environment topography influences the emergence of complex multicellular structures from single cells, which is a fundamental problem of biological, ecological and medical relevance.
