Super-resolution by diffusion models: low-resolution images of microtubules (left) are transformed to high-resolution (right) by diffusion model. Dataset courtesy: BioSR Dataset. (Image by H. Bachimamchi.)Diffusion Models to Enhance the Resolution of Microscopy Images: A Tutorial
Harshith Bachimanchi, Giovanni Volpe
arXiv: 2409.16488
Diffusion models have emerged as a prominent technique in generative modeling with neural networks, making their mark in tasks like text-to-image translation and super-resolution. In this tutorial, we provide a comprehensive guide to build denoising diffusion probabilistic models (DDPMs) from scratch, with a specific focus on transforming low-resolution microscopy images into their corresponding high-resolution versions. We provide the theoretical background, mathematical derivations, and a detailed Python code implementation using PyTorch, along with techniques to enhance model performance.
Propagation of scattered light through a scattering microscope, illustrating typical nanoparticles studied. (Image by B. García Rodriguez.)Optical Label-Free Microscopy Characterization of Dielectric Nanoparticles: A tutorial
Berenice Garcia Rodriguez, Erik Olsén, Fredrik Skärberg, Giovanni Volpe, Fredrik Höök, Daniel Sundås Midtvedt
arXiv: 2409.11810
In order to relate nanoparticle properties to function, fast and detailed particle characterization, is needed. The ability to characterize nanoparticle samples using optical microscopy techniques has drastically improved over the past few decades; consequently, there are now numerous microscopy methods available for detailed characterization of particles with nanometric size. However, there is currently no “one size fits all” solution to the problem of nanoparticle characterization. Instead, since the available techniques have different detection limits and deliver related but different quantitative information, the measurement and analysis approaches need to be selected and adapted for the sample at hand. In this tutorial, we review the optical theory of single particle scattering and how it relates to the differences and similarities in the quantitative particle information obtained from commonly used microscopy techniques, with an emphasis on nanometric (submicron) sized dielectric particles. Particular emphasis is placed on how the optical signal relates to mass, size, structure, and material properties of the detected particles and to its combination with diffusivity-based particle sizing. We also discuss emerging opportunities in the wake of new technology development, with the ambition to guide the choice of measurement strategy based on various challenges related to different types of nanoparticle samples and associated analytical demands.
Sketch of a colloid above a substrate with a bull’s-eye pattern. (Image by the Authors.)Critical Casimir levitation of colloids above a bull’s-eye pattern
Piotr Nowakowski, Nima Farahmand Bafi, Giovanni Volpe, Svyatoslav Kondrat, S. Dietrich
arXiv: 2409.08366
Critical Casimir forces emerge among particles or surfaces immersed in a near-critical fluid, with the sign of the force determined by surface properties and with its strength tunable by minute temperature changes. Here, we show how such forces can be used to trap a colloidal particle and levitate it above a substrate with a bull’s-eye pattern consisting of a ring with surface properties opposite to the rest of the substrate. Using the Derjaguin approximation and mean-field calculations, we find a rich behavior of spherical colloids at such a patterned surface, including sedimentation towards the ring and levitation above the ring (ring levitation) or above the bull’s-eye’s center (point levitation). Within the Derjaguin approximation, we calculate a levitation diagram for point levitation showing the depth of the trapping potential and the height at which the colloid levitates, both depending on the pattern properties, the colloid size, and the solution temperature. Our calculations reveal that the parameter space associated with point levitation shrinks if the system is driven away from a critical point, while, surprisingly, the trapping force becomes stronger. We discuss the application of critical Casimir levitation for sorting colloids by size and for determining the thermodynamic distance to criticality. Our results show that critical Casimir forces provide rich opportunities for controlling the behavior of colloidal particles at patterned surfaces.
The three platforms developed to observe and characterise bacterial collective behaviour in different conditions. (Image by J. Dominguez.)Jesús Manuel Antúnez Domínguez defended his PhD thesis on 6 September 2024. Congrats!
The defense took place in PJ, Institutionen för fysik, Origovägen 6b, Göteborg.
Title: Microscopic approaches for bacterial collective behaviour studies.
Abstract: Bacteria significantly impact our lives, from their beneficial role as probiotics to their involvement in infection environments. Their widespread presence is largely due to their ability to adapt to diverse conditions through collective behavior, which enables the development of complex strategies from the contributions of simple individual entities. However the understanding of these systems is limited by the reach of current study techniques. This work presents the development of three platforms designed to perform microscopic studies and characterise bacterial collective behaviors in situ, profiting the advantages of microfluidics over traditional culture techniques.
The first platform integrates bacterial culture on solid agar directly on the microscope stage, allowing for extended observation periods of up to a week. The agar is housed within an elastomer structure sealed with glass, ensuring environmental isolation while maintaining optical accessibility. This platform was used to document the complex social strategies of Myxococcus xanthus, including motility mechanisms, predation organisation, and fruiting body formation.
The second platform is an automated testing system for quantifying bacterial viability under various conditions. Using microfluidic technology, this platform streamlines and parallelise the process. It adapts the Ames genotoxicity test to a miniaturized version, using microscopy imaging as the readout. This approach reduces experimental turnaround time and minimizes the handling of hazardous substances.
The third platform is a microfluidic system designed for the microscopy observation of bacteria within stabilised droplets. This approach enhances throughput and allows for the production of various types of droplets on the same chip. Bacillus subtilis bacteria were encapsulated in these droplets, and their entire biofilm formation life cycle was observed in detail. Parallel to this, custom software was developed specifically for analysing microscopy images to automatically quantify biofilm formation.
Each of these platforms provides a unique perspectives in the study of bacterial collective behavior to offer a comprehensive toolkit for researchers. complementing one another. This work will equip researchers with the tools to address the mysteries of bacterial collective behavior and opens up new possibilities for application and investigation.
Schematic and brightfield image (inset) of the movement of 16μm diameter micromotor under the illumination of linearly polarized 1064nm laser. (Image by G. Wang.)Light-driven metamachines
Gan Wang, Marcel Rey, Antonio Ciarlo, Mohanmmad Mahdi Shanei, Kunli Xiong, Giuseppe Pesce, Mikael Käll and Giovanni Volpe Date: 5 September 2024 Time: 15:45-16:00
The incorporation of Moore’s law into integrated circuits has spurred opportunities for downsizing traditional mechanical components. Despite advancements in single on-chip motors using electrical, optical, and magnetic drives under ~100 μm, creating complex machines with multiple units remains challenging. Here, we developed a ~10 μm on-chip micromotor using a method compatible with complementary metal oxide semiconductors (CMOS) process. The meta-surface is embedded with the motor to control the incident laser beam direction, enabling momentum exchange with light for movement. The rotation direction and speed are adjustable through the meta-surface, along with the intensity and polarization of applied light. By combining these motors and controlling the configuration, we create complex machines with a size similar to traditional machines below 50um, such as the rotary motion mode of multiple gear coupled gear trains, and the linear motion mode combined with rack and pinion, and combine the micro metal The mirror is introduced into the machine to realize the self-controlled scanning function of the laser in a fixed area.
(Photo by A. Ciarlo.)Erik Olsén started his postdoc at the Physics Department of the University of Gothenburg on 26th August 2024. His research is funded by a Swedish research council internation postdoc fellowship with grant nr 2024-00439.
Erik received a PhD degree 2023 in physics from Chalmers University of Technology, Sweden. In his thesis he focused on optical particle characterisation of nanoparticles and submicron particles, with an emphasis on label-free characterisation methods.
The Soft Matter Lab will administrate the postdoc grant while Erik will be in the lab of Sabrina Leslie at University of British Columbia (UBC). At UBC, Erik will combine different image modalities with confined lens induced confinement (CLiC) to characterise different types of biological nanoparticles.
