Julius B. Kirkegaard

Albert Alonso, Julius B. Kirkegaard

Computer-aided analysis of biological microscopy data has seen a massive improvement with the utilization of general-purpose deep learning techniques. Yet, in microscopy studies of multi-organism systems, the problem of collision and overlap remains challenging. This is particularly true for systems composed of slender bodies such as crawling nematodes, swimming spermatozoa, or the beating of eukaryotic or prokaryotic flagella. Here, we develop a novel end-to-end deep learning approach to extract precise shape trajectories of generally motile and overlapping splines. Our method works in low resolution settings where feature keypoints are hard to define and detect. Detection is fast and we demonstrate the ability to track thousands of overlapping organisms simultaneously. While our approach is agnostic to area of application, we present it in the setting of and exemplify its usability on dense experiments of crawling Caenorhabditis elegans. The model training is achieved purely on synthetic data, utilizing a physics-based model for nematode motility, and we demonstrate the model's ability to generalize from simulations to experimental videos.

Albert Alonso, Julius B. Kirkegaard

We investigate the boundary between chemotaxis driven by spatial estimation of gradients and chemotaxis driven by temporal estimation. While it is well known that spatial chemotaxis becomes disadvantageous for small organisms at high noise levels, it is unclear whether there is a discontinuous switch of optimal strategies or a continuous transition exists. Here, we employ deep reinforcement learning to study the possible integration of spatial and temporal information in an a priori unconstrained manner. We parameterize such a combined chemotactic policy by a recurrent neural network and evaluate it using a minimal theoretical model of a chemotactic cell. By comparing with constrained variants of the policy, we show that it converges to purely temporal and spatial strategies at small and large cell sizes, respectively. We find that the transition between the regimes is continuous, with the combined strategy outperforming in the transition region both the constrained variants as well as models that explicitly integrate spatial and temporal information. Finally, by utilizing the attribution method of integrated gradients, we show that the policy relies on a non-trivial combination of spatially and temporally derived gradient information in a ratio that varies dynamically during the chemotactic trajectories.

Albert Alonso, Julius B. Kirkegaard, Robert G. Endres

Single-cell organisms and various cell types use a range of motility modes when following a chemical gradient, but it is unclear which mode is best suited for different gradients. Here, we model directional decision-making in chemotactic amoeboid cells as a stimulus-dependent actin recruitment contest. Pseudopods extending from the cell body compete for a finite actin pool to push the cell in their direction until one pseudopod wins and determines the direction of movement. Our minimal model provides a quantitative understanding of the strategies cells use to reach the physical limit of accurate chemotaxis, aligning with data without explicit gradient sensing or cellular memory for persistence. To generalize our model, we employ reinforcement learning optimization to study the effect of pseudopod suppression, a simple but effective cellular algorithm by which cells can suppress possible directions of movement. Different pseudopod-based chemotaxis strategies emerge naturally depending on the environment and its dynamics. For instance, in static gradients, cells can react faster at the cost of pseudopod accuracy, which is particularly useful in noisy, shallow gradients where it paradoxically increases chemotactic accuracy. In contrast, in dynamics gradients, cells form de novo pseudopods. Overall, our work demonstrates mechanical intelligence for high chemotaxis performance with minimal cellular regulation.

Reza Karimzadeh, Albert Alonso, Frans Zdyb et al.

Faithful yet compact explanations for vision models remain a challenge, as commonly used dense perturbation masks are often fragmented and overfitted, needing careful post-processing. Here, we present a training-free explanation method that replaces dense masks with smooth tunable contours. A star-convex region is parameterized by a truncated Fourier series and optimized under an extremal preserve/delete objective using the classifier gradients. The approach guarantees a single, simply connected mask, cuts the number of free parameters by orders of magnitude, and yields stable boundary updates without cleanup. Restricting solutions to low-dimensional, smooth contours makes the method robust to adversarial masking artifacts. On ImageNet classifiers, it matches the extremal fidelity of dense masks while producing compact, interpretable regions with improved run-to-run consistency. Explicit area control also enables importance contour maps, yielding a transparent fidelity-area profiles. Finally, we extend the approach to multi-contour and show how it can localize multiple objects within the same framework. Across benchmarks, the method achieves higher relevance mass and lower complexity than gradient and perturbation based baselines, with especially strong gains on self-supervised DINO models where it improves relevance mass by over 15% and maintains positive faithfulness correlations.

Frans Zdyb, Albert Alonso, Julius B. Kirkegaard

Detecting slender, overlapping structures remains a challenge in computational microscopy. While recent coordinate-based approaches improve detection, they often produce less accurate splines than pixel-based methods. We introduce a training-free differentiable rendering approach to spline refinement, achieving both high reliability and sub-pixel accuracy. Our method improves spline quality, enhances robustness to distribution shifts, and shrinks the gap between synthetic and real-world data. Being fully unsupervised, the method is a drop-in replacement for the popular active contour model for spline refinement. Evaluated on C. elegans nematodes, a popular model organism for drug discovery and biomedical research, we demonstrate that our approach combines the strengths of both coordinate- and pixel-based methods.