arXiv subjects

Netta Cohen

Publications and source records attributed to Netta Cohen.

4 recordsLinked to original sources

arXiv2023

The time is ripe to reverse engineer an entire nervous system: simulating behavior from neural interactions

Just like electrical engineers understand how microprocessors execute programs in terms of how transistor currents are affected by their inputs, neuroscientists want to understand behavior production in terms of how neuronal outputs are affected by their inputs and internal states. This dependency of neuronal outputs on inputs can be described by a state-dependent input-output (IO)-function. However, to reliably identify these IO-functions, we need to perturb each input and combinations of inputs while observing all the outputs. Here, we argue that such completeness is possible in C. elegans; a complete description that goes all the way from the activity of every neuron to predict behavior. The established and growing toolkit of optophysiology can non-invasively capture and control every neuron's activity and scale to countless experiments. The information from many such experiments can be pooled while capturing the inter-individual variability because neuronal identity and function are largely conserved across individuals. Just like electrical engineers use transistor IO-functions to simulate program execution, we argue that neuronal IO-functions could be used to simulate the impressive breadth of brain states and behaviors of C. elegans.

q-bio.NC↗

arXiv2023

3D shape reconstruction of semi-transparent worms

3D shape reconstruction typically requires identifying object features or textures in multiple images of a subject. This approach is not viable when the subject is semi-transparent and moving in and out of focus. Here we overcome these challenges by rendering a candidate shape with adaptive blurring and transparency for comparison with the images. We use the microscopic nematode Caenorhabditis elegans as a case study as it freely explores a 3D complex fluid with constantly changing optical properties. We model the slender worm as a 3D curve using an intrinsic parametrisation that naturally admits biologically-informed constraints and regularisation. To account for the changing optics we develop a novel differentiable renderer to construct images from 2D projections and compare against raw images to generate a pixel-wise error to jointly update the curve, camera and renderer parameters using gradient descent. The method is robust to interference such as bubbles and dirt trapped in the fluid, stays consistent through complex sequences of postures, recovers reliable estimates from blurry images and provides a significant improvement on previous attempts to track C. elegans in 3D. Our results demonstrate the potential of direct approaches to shape estimation in complex physical environments in the absence of ground-truth data.

cs.CV↗

arXiv2017

A new computational method for a model of C. elegans biomechanics: Insights into elasticity and locomotion performance

An organism's ability to move freely is a fundamental behaviour in the animal kingdom. To understand animal locomotion requires a characterisation of the material properties, as well as the biomechanics and physiology. We present a biomechanical model of C. elegans locomotion together with a novel finite element method. We formulate our model as a nonlinear initial-boundary value problem which allows the study of the dynamics of arbitrary body shapes, undulation gaits and the link between the animal's material properties and its performance across a range of environments. Our model replicates behaviours across a wide range of environments. It makes strong predictions on the viable range of the worm's Young's modulus and suggests that animals can control speed via the known mechanism of gait modulation that is observed across different media.

physics.bio-ph↗

arXiv2009

Undulatory Locomotion

Undulatory locomotion is a means of self-propulsion that relies on the generation and propagation of waves along a body. As a mode of locomotion it is primitive and relatively simple, yet can be remarkably robust. No wonder then, that it is so prevalent across a range of biological scales from motile bacteria to gigantic prehistoric snakes. Key to understanding undulatory locomotion is the body's interplay with the physical environment, which the swimmer or crawler will exploit to generate propulsion, and in some cases, even to generate the underlying undulations. This review focuses by and large on undulators in the low Reynolds numbers regime, where the physics of the environment can be much more tractable. We review some key concepts and theoretical advances, as well as simulation tools and results applied to selected examples of biological swimmers. In particular, we extend the discussion to some simple cases of locomotion in non-Newtonian media as well as to small animals, in which the nervous system, motor control, body properties and the environment must all be considered to understand how undulations are generated and modulated. To conclude, we review recent progress in microrobotic undulators that may one day become commonplace in applications ranging from toxic waste disposal to minimally invasive surgery.

physics.bio-ph↗