Accurate single-molecule spot detection for image-based spatial transcriptomics with weakly supervised deep learning.

Image-based spatial transcriptomics methods enable transcriptome-scale gene expression measurements with spatial information but require complex, manually tuned analysis pipelines. We present Polaris, an analysis pipeline for image-based spatial transcriptomics that combines deep-learning models for cell segmentation and spot detection with a probabilistic gene decoder to quantify single-cell gene expression accurately. Polaris offers a unifying, turnkey solution for analyzing spatial transcriptomics data from multiplexed error-robust FISH (MERFISH), sequential fluorescence in situ hybridization (seqFISH), or in situ RNA sequencing (ISS) experiments. Polaris is available through the DeepCell software library (https://github.com/vanvalenlab/deepcell-spots) and https://www.deepcell.org.

Accurate single-molecule spot detection for image-based spatial transcriptomics with weakly supervised deep learning.

Image-based spatial transcriptomics methods enable transcriptome-scale gene expression measurements with spatial information but require complex, manually-tuned analysis pipelines. We present Polaris, an analysis pipeline for image-based spatial transcriptomics that combines deep learning models for cell segmentation and spot detection with a probabilistic gene decoder to quantify single-cell gene expression accurately. Polaris offers a unifying, turnkey solution for analyzing spatial transcriptomics data from MERFSIH, seqFISH, or ISS experiments. Polaris is available through the DeepCell software library (https://github.com/vanvalenlab/deepcell-spots) and https://www.deepcell.org.

Entropy production of an active particle in a box.

A run-and-tumble particle in a one-dimensional box (infinite potential well) is studied. The steady state is analytically solved and analyzed, revealing the emergent length scale of the boundary layer where particles accumulate near the walls. The mesoscopic steady state entropy production rate of the system is derived from coupled Fokker-Planck equations with a linear reaction term, resulting in an exact analytic expression. The entropy production density is shown to peak at the walls. Additionally, the derivative of the entropy production rate peaks at a system size proportional to the length scale of the accumulation boundary layer, suggesting that the behavior of the entropy production rate and its derivatives as a function of the control parameter may signify a qualitative behavior change in the physics of active systems, such as phase transitions.

Active diffusion in oocytes nonspecifically centers large objects during prophase I and meiosis I.

Nucleus centering in mouse oocytes results from a gradient of actin-positive vesicle activity and is essential for developmental success. Here, we analyze 3D model simulations to demonstrate how a gradient in the persistence of actin-positive vesicles can center objects of different sizes. We test model predictions by tracking the transport of exogenous passive tracers. The gradient of activity induces a centering force, akin to an effective pressure gradient, leading to the centering of oil droplets with velocities comparable to nuclear ones. Simulations and experimental measurements show that passive particles subjected to the gradient exhibit biased diffusion toward the center. Strikingly, we observe that the centering mechanism is maintained in meiosis I despite chromosome movement in the opposite direction; thus, it can counteract a process that specifically off-centers the spindle. In conclusion, our findings reconcile how common molecular players can participate in the two opposing functions of chromosome centering versus off-centering.

Signatures of motor susceptibility to forces in the dynamics of a tracer particle in an active gel.

We study a model for the motion of a tracer particle inside an active gel, exposing the properties of the van Hove distribution of the particle displacements. Active events of a typical force magnitude can give rise to non-Gaussian distributions having exponential tails or side peaks. The side peaks are predicted to appear when the local bulk elasticity of the gel is large enough and few active sources are dominant. We explain the regimes of the different distributions and study the structure of the side peaks for active sources that are susceptible to the elastic stress that they cause inside the gel. We show how the van Hove distribution is altered by both the duty cycle of the active sources and their susceptibility, and suggest it as a sensitive probe to analyze microrheology data in active systems with restoring elastic forces.

Generalized Archimedes' principle in active fluids.

We show how a gradient in the motility properties of noninteracting pointlike active particles can cause a pressure gradient that pushes a large inert object. We calculate the force on an object inside a system of active particles with position-dependent motion parameters, in one and two dimensions, and show that a modified Archimedes' principle is satisfied. We characterize the system, both in terms of the model parameters and in terms of experimentally measurable quantities: the spatial profiles of the density, velocity and pressure. This theoretical analysis is motivated by recent experiments, which showed that the nucleus of a mouse oocyte (immature egg cell) moves from the cortex to the center due to a gradient of activity of vesicles propelled by molecular motors; it more generally applies to artificial systems of controlled localized activity.

Forces in inhomogeneous open active-particle systems.

We study the force that noninteracting pointlike active particles apply to a symmetric inert object in the presence of a gradient of activity and particle sources and sinks. We consider two simple patterns of sources and sinks that are common in biological systems. We analytically solve a one-dimensional model designed to emulate higher-dimensional systems, and study a two-dimensional model by numerical simulations. We specify when the particle flux due to the creation and annihilation of particles can act to smooth the density profile that is induced by a gradient in the velocity of the active particles, and find the net resultant force due to both the gradient in activity and the particle flux. These results are compared qualitatively to observations of nuclear motion inside the oocyte, that is driven by a gradient in activity of actin-coated vesicles.

Repulsive cues combined with physical barriers and cell-cell adhesion determine progenitor cell positioning during organogenesis.

The precise positioning of organ progenitor cells constitutes an essential, yet poorly understood step during organogenesis. Using primordial germ cells that participate in gonad formation, we present the developmental mechanisms maintaining a motile progenitor cell population at the site where the organ develops. Employing high-resolution live-cell microscopy, we find that repulsive cues coupled with physical barriers confine the cells to the correct bilateral positions. This analysis revealed that cell polarity changes on interaction with the physical barrier and that the establishment of compact clusters involves increased cell-cell interaction time. Using particle-based simulations, we demonstrate the role of reflecting barriers, from which cells turn away on contact, and the importance of proper cell-cell adhesion level for maintaining the tight cell clusters and their correct positioning at the target region. The combination of these developmental and cellular mechanisms prevents organ fusion, controls organ positioning and is thus critical for its proper function.

Desert ants achieve reliable recruitment across noisy interactions.

We study how desert ants, Cataglyphis niger, a species that lacks pheromone-based recruitment mechanisms, inform each other about the presence of food. Our results are based on automated tracking that allows us to collect a large database of ant trajectories and interactions. We find that interactions affect an ant's speed within the nest. Fast ants tend to slow down, whereas slow ones increase their speed when encountering a faster ant. Faster ants tend to exit the nest more frequently than slower ones. So, if an ant gains enough speed through encounters with others, then she tends to leave the nest and look for food. On the other hand, we find that the probability for her to leave the nest depends only on her speed, but not on whether she had recently interacted with a recruiter that has found the food. This suggests a recruitment system in which ants communicate their state by very simple interactions. Based on this assumption, we estimate the information-theoretical channel capacity of the ants' pairwise interactions. We find that the response to the speed of an interacting nest-mate is very noisy. The question is then how random interactions with ants within the nest can be distinguished from those interactions with a recruiter who has found food. Our measurements and model suggest that this distinction does not depend on reliable communication but on behavioural differences between ants that have found the food and those that have not. Recruiters retain high speeds throughout the experiment, regardless of the ants they interact with; non-recruiters communicate with a limited number of nest-mates and adjust their speed following these interactions. These simple rules lead to the formation of a bistable switch on the level of the group that allows the distinction between recruitment and random noise in the nest. A consequence of the mechanism we propose is a negative effect of ant density on exit rates and recruitment success. This is, indeed, confirmed by our measurements.