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We investigate how locomotory behavior is generated in the brain focusing on the paradigmatic connectome of nematode Caenorhabditis elegans (C. elegans) and on neuronal activity patterns that control forward locomotion. We map the neuronal…
Despite the relative simplicity of C. elegans, its locomotion machinery is not yet well understood. We focus on the generation of dorsoventral body bends. While central pattern generators are commonly involved in animal locomotion, their…
Post-genomic research deals with challenging problems in screening genomes of organisms for particular functions or potential for being the targets of genetic engineering for desirable biological features. 'Phenotyping' of wild type and…
The transport of bio-particles in viscous flows exhibits a rich variety of dynamical behaviour, such as morphological transitions, complex orientation dynamics or deformations. Characterising such complex behaviour under well controlled…
How microorganisms respond to and interact with their environment can vary significantly from individual to individual, which can have important microbiological and ecological implications. However, most microscopy techniques can only…
3D cell tracking in a living organism has a crucial role in live cell image analysis. Cell tracking in C. elegans has two difficulties. First, cell migration in a consecutive frame is large since they move their head during scanning.…
The motility of the worm nematode \textit{Caenorhabditis elegans} is investigated in shallow, wet granular media as a function of particle size dispersity and area density ($\phi$). Surprisingly, we find that the nematode's propulsion speed…
Animal habitat surveys play a critical role in preserving the biodiversity of the land. One of the effective ways to gain insights into animal habitats involves identifying animal footprints, which offers valuable information about species…
Objects we encounter often change appearance as we interact with them. Changes in illumination (shadows), object pose, or the movement of non-rigid objects can drastically alter available image features. How do biological visual systems…
Tracking many cells in time-lapse 3D image sequences is an important challenging task of bioimage informatics. Motivated by a study of brain-wide 4D imaging of neural activity in C. elegans, we present a new method of multi-cell tracking.…
The millimeter-long soil-dwelling nematode {\it C. elegans} propels itself by producing undulations that propagate along its body and turns by assuming highly curved shapes. According to our recent study [PLoS ONE \textbf{7}, e40121 (2012)]…
Today, the area of point-of-care diagnostics is synonymous with paper microfluidics where cheap, disposable, and on-the-spot detection toolkits are being developed for a variety of chemical tests. In this work, we present a novel…
Particle tracking is a powerful biophysical tool that requires conversion of large video files into position time series, i.e. traces of the species of interest for data analysis. Current tracking methods, based on a limited set of input…
Animal locomotion is often subject to constraints arising from anatomical/physiological asymmetries. We use the nematode C.~elegans as a minimal model system to ask whether such constraints might shape locomotion patterns optimized during…
Field-captured video facilitates detailed studies of spatio-temporal aspects of animal locomotion, decision-making and environmental interactions including predator-prey relationships and habitat utilisation. But even though data capture is…
We develop a stochastic whole-brain and body simulator of the nematode roundworm Caenorhabditis elegans (C. elegans) and show that it is sufficiently regularizing to allow imputation of latent membrane potentials from partial calcium…
We exploit the reduced space of C. elegans postures to develop a novel tracking algorithm which captures both simple shapes and also self-occluding coils, an important, yet unexplored, component of worm behavior. We apply our algorithm to…
Studies of social and group behavior in interacting organisms require high-throughput analysis of the motion of a large number of individual subjects. Computer vision techniques offer solutions to specific tracking problems, and allow…
Computational approaches which emulate in-vivo nervous system are needed to investigate mechanisms of the brain to orchestrate behavior. Such approaches must integrate a series of biophysical models encompassing the nervous system, muscles,…
We present a new approach for understanding the periodicity structure and semantics of motion datasets, independently of the morphology and skeletal structure of characters. Unlike existing methods using an overly sparse high-dimensional…