Single-shot self-supervised object detection in microscopy published in Nature Communications

LodeSTAR tracks the plankton Noctiluca scintillans. (Image by the Authors of the manuscript.)
Single-shot self-supervised particle tracking
Benjamin Midtvedt, Jesús Pineda, Fredrik Skärberg, Erik Olsén, Harshith Bachimanchi, Emelie Wesén, Elin K. Esbjörner, Erik Selander, Fredrik Höök, Daniel Midtvedt, Giovanni Volpe
Nature Communications 13, 7492 (2022)
arXiv: 2202.13546
doi: 10.1038/s41467-022-35004-y

Object detection is a fundamental task in digital microscopy, where machine learning has made great strides in overcoming the limitations of classical approaches. The training of state-of-the-art machine-learning methods almost universally relies on vast amounts of labeled experimental data or the ability to numerically simulate realistic datasets. However, experimental data are often challenging to label and cannot be easily reproduced numerically. Here, we propose a deep-learning method, named LodeSTAR (Localization and detection from Symmetries, Translations And Rotations), that learns to detect microscopic objects with sub-pixel accuracy from a single unlabeled experimental image by exploiting the inherent roto-translational symmetries of this task. We demonstrate that LodeSTAR outperforms traditional methods in terms of accuracy, also when analyzing challenging experimental data containing densely packed cells or noisy backgrounds. Furthermore, by exploiting additional symmetries we show that LodeSTAR can measure other properties, e.g., vertical position and polarizability in holographic microscopy.

Fast and Accurate Nanoparticle Characterization Using Deep-Learning-Enhanced Off-Axis Holography published in ACS Nano

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

Fast and Accurate Nanoparticle Characterization Using Deep-Learning-Enhanced Off-Axis Holography
Benjamin Midtvedt, Erik Olsén, Fredrik Eklund, Fredrik Höök, Caroline Beck Adiels, Giovanni Volpe, Daniel Midtvedt
ACS Nano 15(2), 2240–2250 (2021)
doi: 10.1021/acsnano.0c06902
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.