Invited Seminar by Saga Helgadottir at the Max Planck Institute for the Science of Light, 10 May 2019

Digital video microscopy enhanced by deep learning

Saga Helgadottir
Sandoghdar Division, Max Planck Institute for the Science of Light, Erlangen, Germany
10 May 2019

Single particle tracking is essential in many branches of science and technology, from the measurement of biomolecular forces to the study of colloidal crystals. Standard methods rely on algorithmic approaches; by fine-tuning several user-defined parameters, these methods can be highly successful at tracking a well-defined kind of particle under low-noise conditions with constant and homogenous illumination. Here, we introduce an alternative data-driven approach based on a convolutional neural network, which we name DeepTrack. We show that DeepTrack outperforms algorithmic approaches, especially in the presence of noise and under poor illumination conditions. We use DeepTrack to track an optically trapped particle under very noisy and unsteady illumination conditions, where standard algorithmic approaches fail. We then demonstrate how DeepTrack can also be used to track multiple particles and non-spherical objects such as bacteria, also at very low signal-to-noise ratios. In order to make DeepTrack readily available for other users, we provide a Python software package, which can be easily personalized and optimized for specific applications.

Saga Helgadottir, Aykut Argun & Giovanni Volpe, Optica 6(4), 506—513 (2019)
doi: 10.1364/OPTICA.6.000506
arXiv: 1812.02653
GitHub: DeepTrack

Presentation by Laura Pérez at the OSA Biophotonics Congress, Tucson, 16 Apr 2019

FORMA: Force Reconstruction via Maximum-likelihood-estimator Analysis

Laura Pérez García, Jaime Donlucas Pérez, Giorgio Volpe, Alejandro V. Areola & Giovanni Volpe
OSA Biophotonics Congress, Tucson (AZ), USA
16 April 2019

Microscopic force characterization is often done by using a microscopic colloidal particle which probes local forces. These particles are often held by a harmonic trapping potential with stiffness k so that a homogeneous force acting on the particle results in a displacement Δx from the equilibrium position and the force can, therefore, be measured as k Δx . To perform such measurement, it is necessary to determine the value of k , which is often done by measuring the Brownian fluctuations of the particle around its stable equilibrium position. This is achieved by measuring the particle position as a function of time, x (t) , and then using some calibration algorithms; the most commonly employed techniques are the potential analysis that relies on the fact that the force is derived from a potential; and the power spectral density (PSD) and the auto-correlation function (ACF) methods that require a regular sampling in time. Besides the previous requirements, all methods depend on the choice of some analysis parameters. This has inhibited the applicability of force measurement methods to characterize force fields with non-conservative components or where the particle freely explores an extended potential landscape. We propose a method for Force Reconstruction via Maximum-likelihood-estimator Analysis (FORMA) that exploits the fact that in the proximity of an equilibrium position the force field can be approximated by a linear form and, therefore, optimally estimated using a linear Maximum-likelihood-estimator (MLE).

Session: Biological Applications
10:30 AM–12:00 AM, Tuesday, April 16, 2019

More information can be found on the link: https://www.osapublishing.org/abstract.cfm?uri=OMA-2019-AT2E.2

 

Presentation by Saga Helgadottir at the OSA Biophotonics Congress, Tucson, 16 Apr 2019

Digital video microscopy enhanced by deep learning

Saga Helgadottir, Aykut Argun & Giovanni Volpe
OSA Biophotonics Congress, Tucson (AZ), USA
16 April 2019

Single particle tracking is essential in many branches of science and technology, from the measurement of biomolecular forces to the study of colloidal crystals. Standard methods rely on algorithmic approaches; by fine-tuning several user-defined parameters, these methods can be highly successful at tracking a well-defined kind of particle under low-noise conditions with constant and homogenous illumination. Here, we introduce an alternative data-driven approach based on a convolutional neural network, which we name DeepTrack. We show that DeepTrack outperforms algorithmic approaches, especially in the presence of noise and under poor illumination conditions. We use DeepTrack to track an optically trapped particle under very noisy and unsteady illumination conditions, where standard algorithmic approaches fail. We then demonstrate how DeepTrack can also be used to track multiple particles and non-spherical objects such as bacteria, also at very low signal-to-noise ratios. In order to make DeepTrack readily available for other users, we provide a Python software package, which can be easily personalized and optimized for specific applications.

Session: Biological Applications
10:30 AM–12:00 AM, Tuesday, April 16, 2019

More information can be found on the link: https://www.osapublishing.org/abstract.cfm?uri=OMA-2019-AT2E.5

 

Presentation by F. Schmidt at the OSA Biophotonics Congress, Tucson, 16 Apr 2019

Light-driven Assembly and Optical Manipulation of Active Colloidal Molecules

Falko Schmidt, Benno Liebchen, Hartmut Loewen & Giovanni Volpe
OSA Biophotonics Congress, Tucson (AZ), USA
16 April 2019

Active matter, consisting of self-propelled units locally injecting energy into the system, opens new horizons for the creation of functional soft materials with designable properties. Experiencing a constant energy input, allows active matter to self-assemble into phases with a complex architecture and functionality such as living clusters which dynamically form, reshape and break-up but would be forbidden in equilibrium material by the entropy maximization (or free energy minimization) principle. The challenge to control this active self-assembly has evoked widespread efforts typically hinging on an engineering of the properties of individual motile constituents. Here, we provide a different route, where activity occurs as an emergent phenomenon only when individual building blocks bind together, in a way which we control by laser light. Using experiments and simulations of two species of immotile microspheres, we exemplify this route by creating active molecules featuring a complex array of behaviors, becoming migrators, spinners and rotators. The possibility to control the dynamics of active self-assembly via light-controllable nonreciprocal interactions will inspire new approaches to understand living matter and to design active materials.

Session: Nanothermodynamics
8:00 AM–10:00 AM, Tuesday, April 16, 2019
Chair: Agnese Callegari; Bilkent University, Turkey

Presentation by Alessandro Magazzù at the OSA Biophotonics Congress, Tucson, 16 Apr 2019

Dynamics of optically trapped particles tuned by critical Casimir forces and torques

Alessandro Magazzù, Agnese Callegari, Juan Pablo Staforelli, Andrea Gambassi, Siegfried Dietrich & Giovanni Volpe.
OSA Biophotonics Congress, Tucson (AZ), USA 16 April 2019

Fluctuations have always played a crucial role in physics, especially when spatially confined by objects. Density fluctuations of the composition of a binary critical mixture emerge when its temperature is in proximity of the critical point. If these fluctuations are confined between two objects (e.g., two colloids, or a colloid and a planar surface), they give rise to Critical Casimir forces (CCFs). Although, these forces were predicted theoretically in 1978 in analogy to quantum-electrodynamical (QED) Casimir Forces they have never aroused a lot of attentions. They have always been considered mostly like a curiosity, until recently. Thanks to the development of nano-technology, CCFs seem to have establish their role in nano-science. They have been measured only recently, proving their relevance at nanoscale.

Session: Enhancing Techniques
14:00 –16:00, Tuesday, April 16, 2019
Chair: Frank Cichos; University Leipzig, Germany

 

Presentation by A. Argun at OSA Life Sciences Conference, Tucson, 14-17 April 2019

Statistics of Brownian particles held in non-harmonic potentials in an active bath

Aykut Argun and Giovanni Volpe
OSA Life Sciences Conference,
Tucson, 14-17 April 2019

Abstract: 

Active systems are subject to persistent noise that arise from biological media or artificial activity like self-propelled particles. Therefore, these systems are  intrinsically out of equilibrium and can only be studied within the framework of non-equilibrium physics. So far, steady-state behavior and dynamical fluctuations of Brownian particles in active baths have been investigated both theoretically and experimentally. While some of the equilibrium properties can be retained by using an effective temperature, for most systems this generalization is not possible. Here, we extend the existing studies to non-harmonic potential cases, where other qualitative distinctions of the active matter emerge.

Invited talk by G. Volpe at the 10th Nordic Workshop on Statistical Physics, Stockholm, 20-22 Mar 2019

Soft Matter Meets Deep Learning
Giovanni Volpe
The 10th Nordic Workshop on Statistical Physics: Biological, Complex and Non-equilibrium Systems, NORDITA, Stockholm, Sweden
20-22 March 2019

I will present an overview of recent projects where we have proposed new approaches to the experimental study of active matter. In particular, I will present a new algorithm for the measurement of microscopic force fields and a deep-learning approach to the tracking of microscopic particles.

Presentation by F. Schmidt at the Gothenburg Nanophotonic Symposium, 26 Mar 2019

Gothenburg Nanophotonic Symposium 2019

The first symposium on the topic of Nanophotonics brings together researchers from physics and chemistry departments in Gothenburg to present their work and share ideas.

Organised by Dr. R. Verre from the Bionanophotonic group at Chalmers University of Technology seven different groups will be present among which F. Schmidt will represent our Softmatter division of Gothenburg University.

The symposium will take place on the 26th of March 2019 at Kollektorn in MC2, Chalmers Campus. Everybody is welcome to attend!

Seminar by G. Volpe at Tel Aviv University, 6 Mar 2019

Emergent Complex Behaviour in Active Matter
Giovanni Volpe
Light Matter Interaction Center, Tel Aviv University, Israel
6 March 2019

After a brief introduction of active particles, I’ll present some recent advances on the study of active particles in complex and crowded environments.
First, I’ll show that active particles can work as microswimmers and microengines powered by critical fluctuations and controlled by light.
Then, I’ll discuss some examples of behavior of active particles in crowded environments: a few active particles alter the overall dynamics of a system; active particles create metastable clusters and channels; active matter leads to non-Boltzmann distributions and alternative non-equilibrium relations; and active colloidal molecules can be created and controlled by light.
Finally, I’ll present some examples of the behavior of active particles in complex environments: active particles often perform 2D active Brownian motion; active particles at liquid-liquid interfaces behave as active interstitials or as active atoms; and the environment alters the optimal search strategy for active particles in complex topologies.