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Ligeralde, A.

Publications and source records attributed to Ligeralde, A..

2 recordsLinked to original sources

Sparse coding models predict a spectral bias in the development of primary visual cortex (V1) receptive fields

It is well known that sparse coding models trained on natural images learn basis functions whose shapes resemble the receptive fields (RFs) of simple cells in the primary visual cortex (V1). However, few studies have considered how these basis functions develop during training. In particular, it is unclear whether certain types of basis functions emerge more quickly than others, or whether they develop simultaneously. In this work, we train an overcomplete sparse coding model (Sparsenet) on natural images and find that there is indeed order in the development of its basis functions, with basis functions tuned to lower spatial frequencies emerging earlier and higher spatial frequency basis functions emerging later. We observe the same trend in a biologically plausible sparse coding model (SAILnet) that uses leaky integrate-and-fire neurons and synaptically local learning rules, suggesting that this result is a general feature of sparse coding. Our results are consistent with recent experimental evidence that the distribution of optimal stimuli for driving neurons to fire shifts towards higher frequencies during normal development in mouse V1. Our analysis of sparse coding models during training yields an experimentally testable prediction for V1 development that this shift may be due in part to higher spatial frequency RFs emerging later, as opposed to a global shift towards higher frequencies across all RFs, which may also play a role. We also find that at least two explanations could account for the order of RF development: 1) high frequency RFs require more information to be specified accurately, and thus may require more visual experience in order to learn, and 2) early development of low frequency RFs improves the sparseness and fidelity of the visual representation more than early development of high frequency RFs. Author summaryWe are interested in how visual neurons learn representations of the natural world. In particular, we want to know whether certain visual features are learned by the visual cortex earlier in development than others. To address this question, we turn to a class of algorithms that can learn to represent natural scenes in a sparse fashion, with only a few neurons active at any given time (population sparseness). While sparse coding has been used extensively to model the response properties of neurons in the visual cortex, we use it here to arrive at a quantitative description of the way neurons might learn to encode visual information during development. We find that receptive fields (RFs) tuned to lower spatial frequencies develop earlier in our sparse coding models compared to high frequency RFs. If our prediction is accurate, such a description would provide a general framework for understanding the development of the functional properties of V1 neurons and serve as a guide for future experimental studies. It could also lead to new computational models that learn from input statistics, as well as advances in the design of devices that can augment or replace human vision.

neuroscience↗

cytoNet: Network Analysis of Cell Communities

We introduce cytoNet, a cloud-based tool to characterize cell populations from microscopy images. cytoNet quantifies spatial topology and functional relationships in cell communities using principles of network science. Capturing multicellular dynamics through graph features, cytoNet also evaluates the effect of cell-cell interactions on individual cell phenotypes. We demonstrate cytoNets capabilities in four case studies: 1) characterizing the temporal dynamics of neural progenitor cell communities during neural differentiation, 2) identifying communities of pain-sensing neurons in vivo, 3) capturing the effect of cell community on endothelial cell morphology, and 4) investigating the effect of laminin 4 on perivascular niches in adipose tissue. The analytical framework introduced here can be used to study the dynamics of complex cell communities in a quantitative manner, leading to a deeper understanding of environmental effects on cellular behavior. The versatile, cloud-based format of cytoNet makes the image analysis framework accessible to researchers across domains. Availability and ImplementationQutubLab.org/how | cytoNet contact: cytoNetProject@gmail.com Brain Initiative Alliance Toolmaker cytoNet site: https://www.braininitiative.org/toolmakers/resources/cytonet/ Author / Lay SummarycytoNet provides an online tool to rapidly characterize relationships between objects within images and video frames. To study complex tissue, cell and subcellular topologies, cytoNet integrates vision science with the mathematical technique of graph theory. This allows the method to simultaneously identify environmental effects on single cells and on network topology. cytoNet has versatile use across neuroscience, stem cell biology and regenerative medicine. cytoNet applications described in this study include: (1) characterizing how sensing pain alters neural circuit activity, (2) quantifying how vascular cells respond to neurotrophic stimuli overexpressed in the brain after injury or exercise, (3) delineating features of fat tissue that may confer resistance to obesity and (4) uncovering structure-function relationships of human stem cells as they transform into neurons.

bioengineering↗