Julius B. Kirkegaard
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View article: Extremal Contours: Gradient-driven contours for compact visual attribution
Extremal Contours: Gradient-driven contours for compact visual attribution Open
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 tha…
View article: Spline Refinement with Differentiable Rendering
Spline Refinement with Differentiable Rendering Open
View article: Modeling full-scale leaf venation networks
Modeling full-scale leaf venation networks Open
The vascular network of leaves, comprising xylem and phloem, is a highly optimized system for the delivery of water, nutrients, and sugars. The design rules for these naturally occurring networks have been studied since the time of Leonard…
View article: Detection limitations of bacteria in tissue samples
Detection limitations of bacteria in tissue samples Open
Aims Successful identification of bacteria in tissue samples requires careful consideration of multiple factors, including sample type and quality, the type of bacteria being detected, and the sensitivity and specificity of the detection m…
View article: Persistent pseudopod splitting is an effective chemotaxis strategy in shallow gradients
Persistent pseudopod splitting is an effective chemotaxis strategy in shallow gradients Open
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 a…
View article: Spline refinement with differentiable rendering
Spline refinement with differentiable rendering Open
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 traini…
View article: Adaptive Node Positioning in Biological Transport Networks
Adaptive Node Positioning in Biological Transport Networks Open
Biological transport networks are highly optimized structures that ensure power-efficient distribution of fluids across various domains, including animal vasculature and plant venation. Theoretically, these networks can be described as spa…
View article: Modeling Full-Scale Leaf Venation Networks
Modeling Full-Scale Leaf Venation Networks Open
The vascular network of leaves, comprising xylem and phloem, is a highly optimized system for the delivery of water, nutrients, and sugars. The design rules for these naturally occurring networks have been studied since the time of Leonard…
View article: Local Clustering and Global Spreading of Receptors for Optimal Spatial Gradient Sensing
Local Clustering and Global Spreading of Receptors for Optimal Spatial Gradient Sensing Open
Spatial information from cell-surface receptors is crucial for processes that require signal processing and sensing of the environment. Here, we investigate the optimal placement of such receptors through a theoretical model that minimizes…
View article: Roles of network topology in the relaxation dynamics of simple chemical reaction network models
Roles of network topology in the relaxation dynamics of simple chemical reaction network models Open
Understanding the relationship between the structure of chemical reaction networks and their reaction dynamics is essential for unveiling the design principles of living organisms. However, while some network-structural features are known …
View article: Persistent pseudopod splitting is an effective chemotaxis strategy in shallow gradients
Persistent pseudopod splitting is an effective chemotaxis strategy in shallow gradients Open
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 a…
View article: Learning optimal integration of spatial and temporal information in noisy chemotaxis
Learning optimal integration of spatial and temporal information in noisy chemotaxis Open
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…
View article: Spontaneous breaking of symmetry in overlapping cell instance segmentation using diffusion models
Spontaneous breaking of symmetry in overlapping cell instance segmentation using diffusion models Open
Instance segmentation is the task of assigning unique identifiers to individual objects in images. Solving this task requires breaking the inherent symmetry that semantically similar objects must result in distinct outputs. Deep learning a…
View article: Learning optimal integration of spatial and temporal information in noisy chemotaxis
Learning optimal integration of spatial and temporal information in noisy chemotaxis Open
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…
View article: Fast detection of slender bodies in high density microscopy data
Fast detection of slender bodies in high density microscopy data Open
View article: Spontaneous breaking of symmetry in overlapping cell instance segmentation using diffusion models
Spontaneous breaking of symmetry in overlapping cell instance segmentation using diffusion models Open
Instance segmentation is the task of assigning unique identifiers to individual objects in images. Solving this task requires breaking the inherent symmetry that semantically similar objects must result in distinct outputs. Deep learning a…
View article: Deeptangle Dataset: Labelled Experimental and Synthetic Videos of Swimming and Overlapping C. elegans worms
Deeptangle Dataset: Labelled Experimental and Synthetic Videos of Swimming and Overlapping C. elegans worms Open
This repository contains the dataset employed in the paper Fast spline detection in high density microscopy data.\n\nThree files are provided:\n\n1. videos.zip: raw experimental videos.\n2. labeled_data.zip: labelled sections of experiment…
View article: Deeptangle Dataset: Labelled Experimental and Synthetic Videos of Swimming and Overlapping C. elegans worms
Deeptangle Dataset: Labelled Experimental and Synthetic Videos of Swimming and Overlapping C. elegans worms Open
This repository contains the dataset employed in the paper Fast spline detection in high density microscopy data. Three files are provided: 1. videos.zip: raw experimental videos. 2. labeled_data.zip: labelled sections of…
View article: Protocol to assess metabolic activity of Pseudomonas aeruginosa by measuring heat flow using isothermal calorimetry
Protocol to assess metabolic activity of Pseudomonas aeruginosa by measuring heat flow using isothermal calorimetry Open
Here, we present a protocol for assessing metabolic activity of bacterial populations by measuring heat flow using isothermal calorimetry. We outline the steps for preparing the different growth models of Pseudomonas aeruginosa and perform…
View article: Epigenetic switching with asymmetric bridging interactions
Epigenetic switching with asymmetric bridging interactions Open
View article: Emerging diversity in a population of evolving intransitive dice
Emerging diversity in a population of evolving intransitive dice Open
Exploiting the mathematical curiosity of intransitive dice, we present a simple theoretical model for coevolution that captures scales ranging from the genome of the individual to the system-wide emergence of species diversity. We study a …
View article: Cyclic-di-GMP signaling controls metabolic activity in Pseudomonas aeruginosa
Cyclic-di-GMP signaling controls metabolic activity in Pseudomonas aeruginosa Open
Bacteria in biofilms are embedded in extracellular matrix and display low metabolic activity, partly due to insufficient diffusive exchange of metabolic substrate. The extracellular matrix and low metabolic activity both contribute to the …
View article: Curvature strains as a global orchestrator of morphogenesis
Curvature strains as a global orchestrator of morphogenesis Open
Successful morphogenesis on the scale of organs or organisms requires strict coordination between the constituent cells whose action on the local scale must be orchestrated accurately to achieve a functional shape on the global scale. We p…
View article: Structural determinants of relaxation dynamics in chemical reaction networks
Structural determinants of relaxation dynamics in chemical reaction networks Open
Understanding the relationship between the structure of chemical reaction networks and their reaction dynamics is essential for unveiling the design principles of living organisms. However, while some network-structural features are known …
View article: Simultant: simultaneous curve fitting of functions and differential equations using analytical gradient calculations
Simultant: simultaneous curve fitting of functions and differential equations using analytical gradient calculations Open
View article: Transcriptomic fingerprint of bacterial infection in lower extremity ulcers
Transcriptomic fingerprint of bacterial infection in lower extremity ulcers Open
Clinicians and researchers utilize subjective, clinical classification systems to stratify lower extremity ulcer infections for treatment and research. The purpose of this study was to examine whether these clinical classifications are ref…
View article: Transcriptomic Fingerprint of Bacterial Infection in Lower Extremity Ulcers
Transcriptomic Fingerprint of Bacterial Infection in Lower Extremity Ulcers Open
Clinicians and researchers utilize subjective classification systems based on clinical parameters to stratify lower extremity ulcer infections for treatment and research. This study compared clinical infection classifications (mild to seve…
View article: Superspreading quantified from bursty epidemic trajectories
Superspreading quantified from bursty epidemic trajectories Open
View article: Superspreading of airborne pathogens in a heterogeneous world
Superspreading of airborne pathogens in a heterogeneous world Open
View article: Comparative Studies in the A30P and A53T α-Synuclein C. elegans Strains to Investigate the Molecular Origins of Parkinson's Disease
Comparative Studies in the A30P and A53T α-Synuclein C. elegans Strains to Investigate the Molecular Origins of Parkinson's Disease Open
The aggregation of α-synuclein is a hallmark of Parkinson's disease (PD) and a variety of related neurological disorders. A number of mutations in this protein, including A30P and A53T, are associated with familial forms of the disease. Pa…