Diagnosis of a genetic disease improves with machine learning, a summary in Swedish published in Fysikaktuellt

Neural networks consist of a series of connected layers of neurons, whose connection weights are adjusted to learn how to determine the diagnosis from the input data.

A summary in Swedish of our previously published article “Virtual genetic diagnosis for familial hypercholesterolemia powered by machine learning” has been published in Fysikaktuellt, the journal of the Swedish Physical Society (Svenska fysikersamfundet).

Article: “Diagnostisering av sjukdomar förbättras med maskininlärning”, Saga Helgadottir, Giovanni Volpe and Stefano Romeo (in Swedish)

Original article: Virtual genetic diagnosis for familial hypercholesterolemia powered by machine learning

Press release: 
Algoritm lär sig diagnostisera genetisk sjukdom (in Swedish)
An algorithm that learns to diagnose genetic disease (in English)

Invited talk by G. Volpe at SCOP2020, 25 September 2020

Student Conference on Optics and Photonics (SCOP), organized by the OSA student chapter of the Physical Research Laboratory, Ahmedabad, India.

Giovanni Volpe will give an online invited presentation at the Student Conference on Optics and Photonics (SCOP), organized by the OSA student chapter of Physical Research Laboratory, Ahmedabad, India.

The conference addresses various topics in optics with an emphasis on non linear optics and quantum optics, will be held during 23-25 September, 2020 at the Physical Research Laboratory (PRL), Ahmedabad, India.
The conference includes invited talks by eminent scientists from India and abroad, as well as posters and oral presentations by student participants and research fellows.

The contribution of Giovanni Volpe will be presented according to the following schedule:

Giovanni Volpe
Deep Learning for microscopy and optical trapping
Date: 25 September 2020
Time: 15:10 IST (GMT+5:30)
Place: Online

Non-equilibrium properties of an active nanoparticle in a harmonic potential on ArXiv

Non-spherical nanoparticle held by optical tweezers. The particle is trapped against the cover slide.

Non-equilibrium Properties of an Active Nanoparticle in a Harmonic Potential
Falko Schmidt, Hana Šípovà-Jungová, Mikael Käll, Alois Würger & Giovanni Volpe
arXiv: 2009.08393

Active particles break out of thermodynamic equilibrium thanks to their directed motion, which leads to complex and interesting behaviors in the presence of confining potentials. When dealing with active nanoparticles, however, the overwhelming presence of rotational diffusion hinders directed motion, leading to an increase of their effective temperature, but otherwise masking the effects of self-propulsion. Here, we demonstrate an experimental system where an active nanoparticle immersed in a critical solution and held in an optical harmonic potential features far-from-equilibrium behavior beyond an increase of its effective temperature. When increasing the laser power, we observe a cross-over from a Boltzmann distribution to a non-equilibrium state, where the particle performs fast orbital rotations about the beam axis. These findings are rationalized by solving the Fokker-Planck equation for the particle’s position and orientation in terms of a moment expansion. The proposed self-propulsion mechanism results from the particle’s non-sphericity and the lower critical point of the solute.

E-workshop: Novel Features and Applications of Optical Manipulation

The School of Nano Science, IPM, Tehran, Iran, with the support of IASBS, Zanjan, Iran, is organizing a one-day e-workshop on
Novel Features and Applications of Optical Manipulation
on September 8th, 2020.

The workshop will address the latest features of optical manipulation. Distinguished lecturers in the field will present exciting aspects and applications of optical manipulation along with providing educational outreach to students.

The workshop is open to all and it is free, but pre-registration is required. Registration dates: between 10 and 25 August.

Invited lecturers:
Prof. Kishan Dolakia
Prof. Giovanni Volpe
Prof. Onofrio Maragò
Dr. Valentina Emiliani
Dr. Samaneh Rezvani
Dr. Fatemeh Kalandarifard

Dr. Alireza Moradi
Prof. Reza Asgari

Date: 8 September 2020
Link: Workshop Homepage, Registration

Soft Matter Lab presentations at the SPIE Optics+Photonics Digital Forum

Seven members of the Soft Matter Lab (Saga HelgadottirBenjamin Midtvedt, Aykut Argun, Laura Pérez-GarciaDaniel MidtvedtHarshith BachimanchiEmiliano Gómez) were selected for oral and poster presentations at the SPIE Optics+Photonics Digital Forum, August 24-28, 2020.

The SPIE digital forum is a free, online only event.
The registration for the Digital Forum includes access to all presentations and proceedings.

The Soft Matter Lab contributions are part of the SPIE Nanoscience + Engineering conferences, namely the conference on Emerging Topics in Artificial Intelligence 2020 and the conference on Optical Trapping and Optical Micromanipulation XVII.

The contributions being presented are listed below, including also the presentations co-authored by Giovanni Volpe.

Note: the presentation times are indicated according to PDT (Pacific Daylight Time) (GMT-7)

Emerging Topics in Artificial Intelligence 2020

Saga Helgadottir
Digital video microscopy with deep learning (Invited Paper)
26 August 2020, 10:30 AM
SPIE Link: here.

Aykut Argun
Calibration of force fields using recurrent neural networks
26 August 2020, 8:30 AM
SPIE Link: here.

Laura Pérez-García
Deep-learning enhanced light-sheet microscopy
25 August 2020, 9:10 AM
SPIE Link: here.

Daniel Midtvedt
Holographic characterization of subwavelength particles enhanced by deep learning
24 August 2020, 2:40 PM
SPIE Link: here.

Benjamin Midtvedt
DeepTrack: A comprehensive deep learning framework for digital microscopy
26 August 2020, 11:40 AM
SPIE Link: here.

Gorka Muñoz-Gil
The anomalous diffusion challenge: Single trajectory characterisation as a competition
26 August 2020, 12:00 PM
SPIE Link: here.

Meera Srikrishna
Brain tissue segmentation using U-Nets in cranial CT scans
25 August 2020, 2:00 PM
SPIE Link: here.

Juan S. Sierra
Automated corneal endothelium image segmentation in the presence of cornea guttata via convolutional neural networks
26 August 2020, 11:50 AM
SPIE Link: here.

Harshith Bachimanchi
Digital holographic microscopy driven by deep learning: A study on marine planktons (Poster)
24 August 2020, 5:30 PM
SPIE Link: here.

Emiliano Gómez
BRAPH 2.0: Software for the analysis of brain connectivity with graph theory (Poster)
24 August 2020, 5:30 PM
SPIE Link: here.

Optical Trapping and Optical Micromanipulation XVII

Laura Pérez-García
Reconstructing complex force fields with optical tweezers
24 August 2020, 5:00 PM
SPIE Link: here.

Alejandro V. Arzola
Direct visualization of the spin-orbit angular momentum conversion in optical trapping
25 August 2020, 10:40 AM
SPIE Link: here.

Isaac Lenton
Illuminating the complex behaviour of particles in optical traps with machine learning
26 August 2020, 9:10 AM
SPIE Link: here.

Fatemeh Kalantarifard
Optical trapping of microparticles and yeast cells at ultra-low intensity by intracavity nonlinear feedback forces
24 August 2020, 11:10 AM
SPIE Link: here.

Note: the presentation times are indicated according to PDT (Pacific Daylight Time) (GMT-7)

Optical trapping and critical Casimir forces on ArXiv

Measuring the dynamics of colloids interacting with critical Casimir interaction via blinking optical tweezers: graphical representation of the optical traps.

Optical trapping and critical Casimir forces
Agnese Callegari, Alessandro Magazzù, Andrea Gambassi & Giovanni Volpe
arXiv: 2008.01537

Critical Casimir forces emerge between objects, such as colloidal particles, whenever their surfaces spatially confine the fluctuations of the order parameter of a critical liquid used as a solvent. These forces act at short but microscopically large distances between these objects, reaching often hundreds of nanometers. Keeping colloids at such distances is a major experimental challenge, which can be addressed by the means of optical tweezers. Here, we review how optical tweezers have been successfully used to quantitatively study critical Casimir forces acting on particles in suspensions. As we will see, the use of optical tweezers to experimentally study critical Casimir forces can play a crucial role in developing nano-technologies, representing an innovative way to realize self-assembled devices at the nano- and microscale.

Holographic characterisation of subwavelength particles enhanced by deep learning on ArXiv

Phase and amplitude signals from representative particles for testing the performance of the Deep-learning approach

Holographic characterisation of subwavelength particles enhanced by deep learning
Benjamin Midtvedt, Erik Olsén, Fredrik Eklund, Fredrik Höök, Caroline Beck Adiels, Giovanni Volpe, Daniel Midtvedt
arXiv: 2006.11154

The characterisation of the physical properties of nanoparticles in their native environment plays a central role in a wide range of fields, from nanoparticle-enhanced drug delivery to environmental nanopollution assessment. Standard optical approaches require long trajectories of nanoparticles dispersed in a medium with known viscosity to characterise their diffusion constant and, thus, their size. However, often only short trajectories are available, while the medium viscosity is unknown, e.g., in most biomedical applications. In this work, we demonstrate a label-free method to quantify size and refractive index of individual subwavelength particles using two orders of magnitude shorter trajectories than required by standard methods, and without assumptions about the physicochemical properties of the medium. We achieve this by developing a weighted average convolutional neural network to analyse the holographic images of the particles. As a proof of principle, we distinguish and quantify size and refractive index of silica and polystyrene particles without prior knowledge of solute viscosity or refractive index. As an example of an application beyond the state of the art, we demonstrate how this technique can monitor the aggregation of polystyrene nanoparticles, revealing the time-resolved dynamics of the monomer number and fractal dimension of individual subwavelength aggregates. This technique opens new possibilities for nanoparticle characterisation with a broad range of applications from biomedicine to environmental monitoring.

Enhanced force-field calibration via machine learning on ArXiv

Calibration of a harmonic potential using a recurrent neural network (RNN)

Enhanced force-field calibration via machine learning
Aykut Argun, Tobias Thalheim, Stefano Bo, Frank Cichos, Giovanni Volpe
arXiv: 2006.08963

The influence of microscopic force fields on the motion of Brownian particles plays a fundamental role in a broad range of fields, including soft matter, biophysics, and active matter. Often, the experimental calibration of these force fields relies on the analysis of the trajectories of these Brownian particles. However, such an analysis is not always straightforward, especially if the underlying force fields are non-conservative or time-varying, driving the system out of thermodynamic equilibrium. Here, we introduce a toolbox to calibrate microscopic force fields by analyzing the trajectories of a Brownian particle using machine learning, namely recurrent neural networks. We demonstrate that this machine-learning approach outperforms standard methods when characterizing the force fields generated by harmonic potentials if the available data are limited. More importantly, it provides a tool to calibrate force fields in situations for which there are no standard methods, such as non-conservative and time-varying force fields. In order to make this method readily available for other users, we provide a Python software package named DeepCalib, which can be easily personalized and optimized for specific applications.

Seminar by G. Volpe at ICFO, 16 June 2020

Lucky Encounters: From Optical Tweezers to deep Learning
Giovanni Volpe
ICFO Alumni Seminar (Online)
16 June 2020

In this semi-autobiographical talk, I will look back at my career and its evolution. It all started at ICFO with a PhD on optical tweezers in 2008. It then continued with a series of diverse research projects on different fields: active matter, stochastic thermodynamics, neurosciences and, finally, deep learning. I will emphasize how my career has been shaped by lucky encounters. Encounters that have taken me to places and topics I’d never have imagined beforehand. But it all makes sense, in insight.

Date: 16 June 2020
Time: 15:00
Place: Online

Anisotropic dynamics of a self-assembled colloidal chain in an active bath published on Soft Matter

Bright-field microscopy image of a magnetic chain trapped at the liquid-air interface in a bacterial bath

Anisotropic dynamics of a self-assembled colloidal chain in an active bath
Mehdi Shafiei Aporvari, Mustafa Utkur, Emine Ulku Saritas, Giovanni Volpe & Joakim Stenhammar
Soft Matter, 2020, Advance Article
doi: https://doi.org/10.1039/D0SM00318B
arXiv: 2002.09961

Anisotropic macromolecules exposed to non-equilibrium (active) noise are very common in biological systems, and an accurate understanding of their anisotropic dynamics is therefore crucial. Here, we experimentally investigate the dynamics of isolated chains assembled from magnetic microparticles at a liquid–air interface and moving in an active bath consisting of motile E. coli bacteria. We investigate both the internal chain dynamics and the anisotropic center-of-mass dynamics through particle tracking. We find that both the internal and center-of-mass dynamics are greatly enhanced compared to the passive case, i.e., a system without bacteria, and that the center-of-mass diffusion coefficient D features a non-monotonic dependence as a function of the chain length. Furthermore, our results show that the relationship between the components of D parallel and perpendicular with respect to the direction of the applied magnetic field is preserved in the active bath compared to the passive case, with a higher diffusion in the parallel direction, in contrast to previous findings in the literature. We argue that this qualitative difference is due to subtle differences in the experimental geometry and conditions and the relative roles played by long-range hydrodynamic interactions and short-range collisions.