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Colloquium by G. Volpe at TU-Darmstadt, 18 June 2021, Online

Deep learning for particle tracking. (Image by Aykut Argun)
Deep learning for microscopy, optical trapping, and active matter

Giovanni Volpe
Colloquium
(online at) TU-Darmstadt, Germany
18 June 2021, 14:00 CEST

After a brief overview of artificial intelligence, machine learning and deep learning, I will present a series of recent works in which we have employed deep learning for applications in photonics and active matter.
In particular, I will explain how we employed deep learning to enhance digital video microscopy, to estimate the properties of anomalous diffusion, to characterize microscopic force fields, to improve the calculation of optical forces, and to characterize nanoparticles.
Finally, I will provide an outlook for the application of deep learning in photonics and active matter.

Saga Helgadottir defended her PhD Thesis in Physics on June 16, 2021. Congrats!

Digital video microscopy enhanced by deep learning
Saga Helgadottir defended her PhD Thesis in Physics on June 16, 2021. Congrats!

The disputation took place at 9 a.m. digitally via Zoom. A link to the Zoom meeting was published the day before dissertation on the GU website.

Title:  Deep Learning Applications – From image analysis to medical diagnosis

Abstract:
Deep learning is a subcategory of machine learning and artificial intelligence. Instead of using explicit rules to perform a desired task as in standard algorithmic approaches, machine-learning algorithms autonomously learn from data to determine the rules for the task at hand. The idea of deep learning has been around since the 1950s but was for a long time limited by available computational power and amount of training data. Once overcome these problems, in recent years, deep learning has made great advances in solving various problems.

In this thesis, I show how deep learning can be applied in image analysis and medical diagnosis, while outperforming standard algorithmic methods and simpler machine-learning methods. I begin with showing that a convolutional neural network trained with simulated particle images is able to track experimental single particles, even in poor illumination conditions. I then show how this inspired the development of an all-in-one software to design, train and validate deep-learning solutions for digital microscopy, from particle tracking and characterization in 2D and 3D to the segmentation, characterization and counting of biological cells and image transformation. I show that this software package can be further used to develop a generative adversarial neural network to virtually stain brightfield images of cells, replacing the traditional chemical staining for a downstream analysis of biological features. I then move on from applications in microscopy and image analysis to show the potential of deep learning in medical diagnosis. I show that dense neural networks perform better than simpler machine-learning algorithm and the clinical standard in the diagnosis of a genetic disease and in the prediction of short- and long-term morbidity in patients with congenital-heart-disease. At last, I have shown that a neural network- powered strategy for testing and isolating individuals adapts to the parameters of a disease outbreak achieves an epidemic containment.

The interdisciplinary nature of the work in this thesis has allowed the application of new technologies developed in the field of physics to solve problems in the fields of biology and biomedicine, as well as overcoming barriers for the continued revolutionization of deep learning in microscopy.

Thesishttp://hdl.handle.net/2077/67506

Supervisor: Giovanni Volpe
Examiner: Bernhard Mehlig
Opponent: Carolina Wählby
Committee: Marj Tonini, Maria Garcia-Parajo, Alexander Rohrbach

Screenshots from Saga Helgadottir’s PhD Thesis defense.

PhD Opponent’s presentation.
PhD Thesis presentation: Saga Helgadottir, Giovanni Volpe (Supervisor), Raimund Feifel (GU Physics), Carolina Wählby (Opponent), Marj Tonini (Committee member), Maria Garcia-Parajo (Committee member), Måns Henningson (GU Physics Department Chair), Alexander Rohrbach (Committee member).
PhD Thesis presentation.
PhD Thesis presentation front slide.
PhD Thesis presentation content slide (1).
PhD Thesis presentation content slide (2).
PhD Thesis presentation conclusion slide.
Screenshot from the discussion (1).
Screenshot from the discussion (2).
Screenshot from the discussion (3).

Aykut Argun defended his PhD Thesis in Physics on 14 June 2021. Congrats!

(Image by Aykut Argun)
Aykut Argun defended his Ph.D. thesis on June 14, 2021, at 2 pm CEST. Congrats!

The details of the presentation can be found below. The link to the webinar is announced on the faculty website.

Title: Thermodynamics of microscopic environments: From anomalous diffusion to heat engines.

Abstract:
Unlike their macroscopic counterparts, microscopic systems do not evolve deterministically due to the thermal noise becoming prominent. Such systems are subject to fluctuations that can only be studied within the framework of stochastic thermodynamics. Within the last few decades, the development of stochastic thermodynamics has lead to microscopic heat engines, nonequilibrium relations and the study of anomalous diffusion and active Brownian motion. In this thesis, I experimentally show that the non-Boltzmann statistics emerge in systems that are coupled to an active bath. These non-Boltzmann statistics that result from correlated active noise also disturb the nonequilibrium relations. Nevertheless, I show that these relations can be recovered using an effective potential approach. Next, I demonstrate an experimental realization of a microscopic heat engine. This engine is referred to as the Brownian gyrator, which is coupled to two different heat baths along perpendicular directions. I show that when confined into an elliptical trap that is not aligned with the temperature anisotropy, the Brownian particle is subject to a torque due to the symmetry breaking. This torque creates an autonomous engine whose direction and amplitude can be controlled by tuning the alignment of the elliptical trap. Then, I show that the force fields acting on Brownian particles can be calibrated using a data-driven method that outperforms the existing calibration methods. More importantly, I show that this method, named DeepCalib, can calibrate non-conservative and time-varying force fields that no standard calibration methods exist. Finally, I show that a similar machine-learning-based approach can be used to characterize anomalous diffusion from single trajectories. This method, named RANDI, is very versatile and performs very well in various tasks including classification, inference and segmentation of anomalous diffusion. The work presented in this thesis presents novel experiments that advance microscopic thermodynamics as well as newly developed methods that open up new possibilities in analyzing stochastic trajectories. These findings increased the scientific knowledge at the nexus between microscopic thermodynamics, anomalous diffusion, active matter and machine learning.

Supervisor: Giovanni Volpe
Co-supervisors: Joakim Stenhammar, Mattias Goksör
Examiner: Bernhard Mehlig
Opponent: Juan M. R. Parrondo
Committee: Monika Ritsch-Marte, Sabine H. L. Klapp, Édgar Roldán

Screenshots from Aykut Argun’s PhD Thesis defense.

PhD Thesis Committee, Supervisor, Co-Supervisor, Opponent, and GU Physics Department Chair.
PhD Thesis Committee, Supervisor, Opponent, and GU Physics Department Chair.
PhD Opponent presentation.
PhD Thesis presentation starts.
PhD Thesis front slide.
PhD Thesis content slide.
PhD Thesis final acknowledgment slide.
PhD Thesis final acknowledgment slide.

New PhD position in Physics at Soft Matter Lab: last application day 29 June 2021

Soft Matter Lab is looking for motivated candidates for a new PhD position announced on Tuesday, 8 June 2021.

Last application day: Tuesday, 29 June 2021.
Expected employment starting date: 1 September 2021.

Apply here!    [In English]   [In Swedish]

Excerpt from the announcement

Job assignments:
    Possibility 1: Work at the development of DeepTrack 2.0 (https://aip.scitation.org/doi/10.1063/5.0034891 and https://github.com/softmatterlab/DeepTrack-2.0) in close cooperation with the existing developers’ team at Soft Matter Lab. DeepTrack 2.0 is a software framework we are developing to perform quantitative digital video microscopy using deep learning. The PhD student will actively contribute to the technical design and implementation of the components of DeepTrack. Precisely, the task involves the development, testing and application of optical simulation pipelines for training deep learning networks, as well as the development of collaborative projects with other groups interested in using DeepTrack.
    Possibility 2: Build and operate small robots to study swarm robotics with embedded intelligence. The task involves all stages of design, fabrication, testing and programming the robots for different experiments. The robot models (inspired by the Kilobots https://ssr.seas.harvard.edu/kilobots) are small programmable units capable of motion, short-range communications, neighbor detection and more.

Appointment procedure
Please apply online
The application shall include:
– Cover letter with an explanation of why you apply for the position
– CV including scientific publications
– Copy of exam certificate
– Two referees (name, telephone number, relation)

For the required Qualifications, Eligibility, Assessment criteria, Employment, see the link to the announcement below.

Links:
English: PhD Student in Physics (with focus on machine learning and robotics, Soft Matter Lab)
Swedish: Doktorandplats i Fysik (med fokus på maskininlärning och robotik, Soft Matter Lab)

For further information regarding the position
Giovanni Volpe, Professor, 031-786 9137, giovanni.volpe@physics.gu.se

Olle Fager will defend his Master thesis on 15 June 2021

Olle Fager will defend his Master thesis in MPCAS at the Chalmers University of Technology on 15 June 2021.

Title: Real-Time Multi-Object Tracking and Segmentation with Generated Data using 3D-modelling

Multi-Object Tracking and Segmentation (MOTS) is an important branch of computer vision that has applications in many different areas. In recent developments these methods have been able to reach favorable speed-accuracy trade-offs, making them interesting for real-time applications. In this work different deep learning based MOTS methods have been investigated with the purpose of extending the DeepTrack framework with real-time MOTS capabilities. Deep learning methods rely heavily on the data on which they are trained. The collection and annotation of the data can however be very time-consuming. Therefor, a pipeline is developed and investigated that automatically produces synthetic data by utilizing 3D-modelling. The most accurate tracker achieves a MOTSA score of 94 and the tracker with the best speed-accuracy trade-off achieves a MOTSA score of 88. It is also observed that satisfactory results can be achieved in most situations with a quite general data generation pipeline, indicating that the developed pipeline could be used in different scenarios.

​Name of the master programme: MPCAS – Complex Adaptive Systems
Supervisor: Giovanni Volpe
Examiner: Giovanni Volpe, Department of Physics, University of Gothenburg
Opponent: Arianit Zeqiri and Morad Mahmoudyan

Place: Online via Zoom
Time: 15 June, 2021, 16:00

Presentation by L. Natali at Spatial Data Science 2020, 11 June 2021

Comparison of different evolution regimes of disease spreading: free evolution (bottom left half) vs network strategy (top right half). (Image by Laura Natali.)
Improving epidemic testing and containment strategies using machine learning. 
Laura Natali, Saga Helgadottir, Onofrio M. Maragò, Giovanni Volpe.
Submitted to SDS2020
Date: 11 June
Time: 16:15 (CEST)

Abstract: 
Containment of epidemic outbreaks entails great societal and economic costs.  Cost-effective containment strategies rely on efficiently identifying infected individuals, making the best possible use of the available testing resources. Therefore, quickly identifying the optimal testing strategy is of critical importance. Here, we demonstrate that machine learning can be used to identify which individuals are most beneficial to test, automatically and dynamically adapting the testing strategy to the characteristics of the disease outbreak. Specifically, we simulate an outbreak using the archetypal susceptible-infectious-recovered (SIR) model and we use data about the first confirmed cases to train a neural network that learns to make predictions about the rest of the population. Using these prediction, we manage to contain the outbreak more effectively and more quickly than with standard approaches. Furthermore, we demonstrate how this method can be used also when there is a possibility of reinfection (SIRS model) to efficiently eradicate an endemic disease.

Agaton Fransson defended his Master thesis on 4 June 2021. Congrats!

Agaton Fransson defended his Master thesis in MPCAS at the Chalmers University of Technology on 4 June 2021. Congrats!

Big plankton tracked by network-based software in a sample of big (Strombidium arenicola) and small plankton (Rhodomonas baltica). (Image by Agaton Fransson)
Title: Tracking plankton using neural networks trained on simulated images

Softwares to track particles often use algorithmic approaches to detect particles and to create tracks using the found positions, requiring human fine-tuning of parameters to achieve sought-for results. This can be time consuming and difficult, while also creating opportunities for human error and bias. With the developments of computational power and machine learning techniques such as deep learning, data driven approaches have made their way into many fields of science. Barriers preventing advances of such methods are the lack of available training data within a field and the level of proficiency required to create custom machine learning solutions. DeepTrack 2.0 is a software providing us with means to simulate digital microscopy images, build and train neural networks such as U-nets. In this paper DeepTrack 2.0 is utilized and built on to fit the needs of marine biologists when tracking plankton. Here I show that DeepTrack 2.0 provides us with the tools necessary to detect and track different types of plankton filmed in a variety of conditions with performance on par with and with the potential to outperform conventional tracking softwares. I also show that for plankton in a messy environment moving uniformly a network trained to detect motion rather than a shape proves more successful. These results demonstrate the versatility of deep learning methods and the potential of training networks on simulations for applications on real data, as is the case for marine biologists studying plankton. They also show the impact the structure of the training data has on the nature of the network.

​Name of the master programme: MPCAS – Complex Adaptive Systems
Supervisor: Giovanni Volpe, Daniel Midtvedt
Examiner: Giovanni Volpe, Department of Physics, University of Gothenburg
Opponent: Kevin Rylander

Place: Online via Zoom
Time: 4 June, 2021, 15:00

Kevin Andersson and Eric Lindgren will defend their Master thesis on 2 June 2021

Kevin Andersson and Eric Lindgren will defend their Master thesis on 2 June 2021.

Title: Saliency mapping of RS-fMRI data in GCNs for sex and brain age prediction
Subtitle: Identifying important functional brain networks using explainability in Graph Convolutional Networks

Insights into how biological sex and healthy ageing affects the human brain are important for an increased understanding of the brain. Healthy ageing insights are also useful for clinical applications, for instance in identifying unhealthy ageing due to neurodegenerative disease. To this end, several studies in the last few years have used machine learning methods on neuroscientific data to predict subject sex and brain age. One particularly interesting approach has been to represent functionally connected networks in the brain as graphs, and apply Graph Convolutional Networks (GCNs). To investigate which functional brain networks are connected with sex and age, we develop and analyse GCN-based models that predicts sex and age from resting-state fMRI data. The analysis of the models is done using saliency mapping techniques which gives insight into what functional brain networks in the data are relevant for the predictions. With this approach, we obtain a sex prediction accuracy of up to 79% and an age prediction MAE of 5.9 years. Furthermore, we find indications that the Sensory Motor Network and the cerebellum are among the more important functional brain networks for predicting sex and brain age.

​Master programme: Physics
Supervisor: Alice Neimante Diemante (Syntronic AB)
Examiner: Giovanni Volpe, Department of Physics, University of Gothenburg
Opponent: Rasmus Svensson

Place: Online via Zoom
Time: 2 June, 2021, 16:00

Gustaf Sjösten defended his Master thesis on 17 May 2021. Congrats!

Gustaf Sjösten defended his Master thesis in MPCAS at the Chalmers University of Technology on 17 May 2021. Congrats!

Artistic rendering of a light source illumination a single biomolecule and scattered photons. (Image by Gustaf Sjösten, inspired by an image created by Barbora Spackova)
Title: Deep Learning for Nanofluidic Scattering Microscopy

A novel technique for label-free, real-time characterization of single biomolecules called Nanofluidic Scatter Microscopy (NSM) has recently been developed by the Langhammer research group at Chalmers. We have created a machine learning (ML) framework consisting of deep convolutional neural networks such as U-nets, ResNets and YOLO in order to characterize single biomolecules through kymographs collected through NSM, as an alternative approach to a standard data analysis method (SA). As a laser irradiates visible light onto single biomolecules freely diffusing in solution inside nanofluidic channels, the biomolecule and the nanochannel scatter light coherently into the collection optics, such that the nanochannels improve the optical contrast of the imaged biomolecules by several orders of magnitude. A video of the total scattering intensity is then recorded with a high frame rate camera (capturing 200 fps) in order to capture the movement of the molecules as well as the optical contrast of the biomolecules with respect to the nanochannel. From the movement of one single biomolecule, it is possible to predict its diffusion constant, which can then be used to infer the hydrodynamic radius of the biomolecule. Additionally, the predicted optical contrast of one single biomolecule can in turn be used to infer its molecular weight. From the combination of hydrodynamic radius and molecular weight, information about the conformal state of single biomolecules can be inferred. In this thesis, we show that the ML approach yields results comparable to the SA which was developed independently of the ML technique for biomolecules in the weight span 66-669 kDa, and we also show that the ML technique is superior to the SA in other regards, such as computational speed and potential to characterize smaller molecules. The results of the data analysis performed with the ML framework will also make an appearance in the first paper on the NSM technique which has been submitted for publication and is currently under review.

​Name of the master programme: MPCAS – Complex Adaptive Systems
Supervisor: Giovanni Volpe, Daniel Midtvedt
Examiner: Giovanni Volpe, Department of Physics, University of Gothenburg
Opponent: Anton Jansson

Place: Online via Zoom
Time: 17 May, 2021, 16:00

Seminar by G. Volpe at Vi2, University of Uppsala, 17 May 2021

Deep learning for particle tracking. (Image by Aykut Argun.)
Quantitative Digital Microscopy with Deep Learning
Giovanni Volpe
Seminar
Vi2 Seminar (Visual Information and Interaction)
University of Uppsala
17 May 2021, 14:15 CEST
Online

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.

Bio: Giovanni Volpe is Professor at the Physics Department at the University of Gothenburg (Gothenburg, Sweden), where he has been leading the Soft Matter Lab since 2016. He has established a strong research group of 18 people (3 postdocs, 12 PhD students, 3 Master students, http://www.softmatterlab.org ) with an externally-funded, ambitious and interdisciplinary research program that combines soft condensed matter, optical manipulation, nanotechnology, and machine learning. He has attracted external funding exceeding 6M €, including several national and European grants such as the ERC-StG ComplexSwimmers (2016-2021) and the ERC-CoG MAPEI (2021-2026). He is a co-funder of the startup companies Lucero Bio and IFLAI.

Link: Vi2 Seminars (zoom link included in the webpage)