Browse
Submit Data
Databases
API
Help

Dataset Information

8 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Fitting Splines to Axonal Arbors Quantifies Relationship Between Branch Order and Geometry.

ABSTRACT: Neuromorphology is crucial to identifying neuronal subtypes and understanding learning. It is also implicated in neurological disease. However, standard morphological analysis focuses on macroscopic features such as branching frequency and connectivity between regions, and often neglects the internal geometry of neurons. In this work, we treat neuron trace points as a sampling of differentiable curves and fit them with a set of branching B-splines. We designed our representation with the Frenet-Serret formulas from differential geometry in mind. The Frenet-Serret formulas completely characterize smooth curves, and involve two parameters, curvature and torsion. Our representation makes it possible to compute these parameters from neuron traces in closed form. These parameters are defined continuously along the curve, in contrast to other parameters like tortuosity which depend on start and end points. We applied our method to a dataset of cortical projection neurons traced in two mouse brains, and found that the parameters are distributed differently between primary, collateral, and terminal axon branches, thus quantifying geometric differences between different components of an axonal arbor. The results agreed in both brains, further validating our representation. The code used in this work can be readily applied to neuron traces in SWC format and is available in our open-source Python package brainlit: http://brainlit.neurodata.io/.

SUBMITTER: Athey TL

PROVIDER: S-EPMC8385655 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Tracking individual action potentials throughout mammalian axonal arbors.

Project description:Axons are neuronal processes specialized for conduction of action potentials (APs). The timing and temporal precision of APs when they reach each of the synapses are fundamentally important for information processing in the brain. Due to small diameters of axons, direct recording of single AP transmission is challenging. Consequently, most knowledge about axonal conductance derives from modeling studies or indirect measurements. We demonstrate a method to noninvasively and directly record individual APs propagating along millimeter-length axonal arbors in cortical cultures with hundreds of microelectrodes at microsecond temporal resolution. We find that cortical axons conduct single APs with high temporal precision (~100 µs arrival time jitter per mm length) and reliability: in more than 8,000,000 recorded APs, we did not observe any conduction or branch-point failures. Upon high-frequency stimulation at 100 Hz, successive became slower, and their arrival time precision decreased by 20% and 12% for the 100th AP, respectively.

| S-EPMC5633342 | biostudies-literature

High-Order Spatial Simulation Using Legendre-Like Orthogonal Splines.

Project description:High-order sequential simulation techniques for complex non-Gaussian spatially distributed variables have been developed over the last few years. The high-order simulation approach does not require any transformation of initial data and makes no assumptions about any probability distribution function, while it introduces complex spatial relations to the simulated realizations via high-order spatial statistics. This paper presents a new extension where a conditional probability density function (cpdf) is approximated using Legendre-like orthogonal splines. The coefficients of spline approximation are estimated using high-order spatial statistics inferred from the available sample data, additionally complemented by a training image. The advantages of using orthogonal splines with respect to the previously used Legendre polynomials include their ability to better approximate a multidimensional probability density function, reproduce the high-order spatial statistics, and provide a generalization of high-order simulations using Legendre polynomials. The performance of the new method is first tested with a completely known image and compared to both the high-order simulation approach using Legendre polynomials and the conventional sequential Gaussian simulation method. Then, an application in a gold deposit demonstrates the advantages of the proposed method in terms of the reproduction of histograms, variograms, and high-order spatial statistics, including connectivity measures. The C++ course code of the high-order simulation implementation presented herein, along with an example demonstrating its utilization, are provided online as supplementary material.

| S-EPMC6411132 | biostudies-literature

Large-Scale Mapping of Axonal Arbors Using High-Density Microelectrode Arrays.

Project description:Understanding the role of axons in neuronal information processing is a fundamental task in neuroscience. Over the last years, sophisticated patch-clamp investigations have provided unexpected and exciting data on axonal phenomena and functioning, but there is still a need for methods to investigate full axonal arbors at sufficient throughput. Here, we present a new method for the simultaneous mapping of the axonal arbors of a large number of individual neurons, which relies on their extracellular signals that have been recorded with high-density microelectrode arrays (HD-MEAs). The segmentation of axons was performed based on the local correlation of extracellular signals. Comparison of the results with both, ground truth and receiver operator characteristics, shows that the new segmentation method outperforms previously used methods. Using a standard HD-MEA, we mapped the axonal arbors of 68 neurons in <6 h. The fully automated method can be extended to new generations of HD-MEAs with larger data output and is estimated to provide data of axonal arbors of thousands of neurons within recording sessions of a few hours.

| S-EPMC6742744 | biostudies-literature

Relationship between the geometry patterns of vertebrobasilar artery and atherosclerosis.

Project description:BackgroundThe plaques at the dorsal or lateral wall of basilar artery (BA) are associated with pontine infarcts. We sought to explore the correlations between vertebrobasilar artery geometry and BA plaque locations.MethodsWe retrospectively analyzed the imaging and clinical data of 84 patients with BA atherosclerosis. On three-dimensional time-of-flight images, a side to side diameter difference of bilateral vertebral artery (VA) and BA bending were assessed. The vertebrobasilar artery geometry was qualitatively classified into four basic configurations: Walking, Tuning Fork, Dominant-Lambda, and Hypoplasia-Lambda. On high-resolution magnetic resonance imaging, the plaques were categorized based on the involvement of the ventral, dorsal, or lateral sides of BA wall. The relationships between vertebrobasilar artery geometry parameters and plaque locations were analyzed.ResultsLeft VA dominance was identified in 28(33%) patients, and right VA dominance in 22(26%) patients. BA bending were detected in 49 patients. There were no significant correlations between the diameter difference/ratio of VA diameters and plaque locations, or between BA bending and plaque locations. BA plaques were evenly distributed in the vertebrobasilar arteries with Tuning Fork and Dominant-Lambda configurations. In Hypoplasia-Lambda group, however, plaques were more frequently located at the dorsal wall (58.57%) than at the ventral (14.43%) and lateral wall (26.71%; P = 0.001). In Walking group, the plaques more likely occurred at the lateral (49.79%) and dorsal (35.07%) wall than at the ventral wall (14.86%, P = 0.02).ConclusionsThe geometric configurations of vertebrobasilar artery strongly influence the BA plaque locations. Further prospective studies are warranted to testify whether Hypoplasia-Lambda and Walking configurations are independent risk factors for pontine infarcts.

| S-EPMC5996488 | biostudies-literature

Establishment of a relationship between blastomere geometry and YAP localisation during compaction.

Project description:Precise patterning within the three-dimensional context of tissues, organs and embryos implies that cells can sense their relative position. During preimplantation development, outside and inside cells rely on apicobasal polarity and the Hippo pathway to choose their fate. Despite recent findings suggesting that mechanosensing might be central to this process, the relationship between blastomere geometry (i.e. shape and position) and the Hippo pathway effector YAP remains unknown. We used a highly quantitative approach to analyse information on the geometry and YAP localisation of individual blastomeres of mouse and human embryos. We identified the proportion of exposed cell surface area as most closely correlating with the nuclear localisation of YAP. To test this relationship, we developed several hydrogel-based approaches to alter blastomere geometry in cultured embryos. Unbiased clustering analyses of blastomeres from such embryos revealed that this relationship emerged during compaction. Our results therefore pinpoint the time during early embryogenesis when cells acquire the ability to sense changes in geometry and provide a new framework for how cells might integrate signals from different membrane domains to assess their relative position within the embryo.

| S-EPMC7561472 | biostudies-literature

Neocortical Chandelier Cells Developmentally Shape Axonal Arbors through Reorganization but Establish Subcellular Synapse Specificity without Refinement.

Project description:Diverse types of cortical interneurons (INs) mediate various kinds of inhibitory control mechanisms to balance and shape network activity. Distinct IN subtypes develop uniquely organized axonal arbors that innervate different subcellular compartments of excitatory principal neurons (PNs), which critically contribute to determining their output properties. However, it remains poorly understood how they establish this peculiar axonal organization and synaptic connectivity during development. Here, taking advantage of genetic labeling of IN progenitors, we examined developmental processes of axonal arbors and synaptic connections formed by murine chandelier cells (ChCs), which innervate axon initial segments (AISs) of PNs and thus powerfully regulate their spike generation. Our quantitative analysis by light microscopy revealed that ChCs overgrow and subsequently refine axonal branches as well as varicosities. Interestingly, we found that although a significant number of axonal varicosities are formed off AISs in addition to on AISs, presynaptic markers are predominantly colocalized with those on AISs throughout development. Immunoelectron microscopic (IEM) analysis also demonstrated that only varicosities apposed to AISs contain presynaptic profiles. These results suggest that subcellular synapse specificity of ChCs is genetically predetermined while axonal geometry is shaped through remodeling. Molecular cues localized at AISs may regulate target recognition and synapse formation by ChCs.

| S-EPMC5458751 | biostudies-literature

On the Relationship Between High-Order Linkage Disequilibrium and Epistasis.

Project description:A plausible explanation for statistical epistasis revealed in genome wide association analyses is the presence of high order linkage disequilibrium (LD) between the genotyped markers tested for interactions and unobserved functional polymorphisms. Based on findings in experimental data, it has been suggested that high order LD might be a common explanation for statistical epistasis inferred between local polymorphisms in the same genomic region. Here, we empirically evaluate how prevalent high order LD is between local, as well as distal, polymorphisms in the genome. This could provide insights into whether we should account for this when interpreting results from genome wide scans for statistical epistasis. An extensive and strong genome wide high order LD was revealed between pairs of markers on the high density 250k SNP-chip and individual markers revealed by whole genome sequencing in the Arabidopsis thaliana 1001-genomes collection. The high order LD was found to be more prevalent in smaller populations, but present also in samples including several hundred individuals. An empirical example illustrates that high order LD might be an even greater challenge in cases when the genetic architecture is more complex than the common assumption of bi-allelic loci. The example shows how significant statistical epistasis is detected for a pair of markers in high order LD with a complex multi allelic locus. Overall, our study illustrates the importance of considering also other explanations than functional genetic interactions when genome wide statistical epistasis is detected, in particular when the results are obtained in small populations of inbred individuals.

| S-EPMC6071592 | biostudies-other

Longitudinal in vivo imaging reveals balanced and branch-specific remodeling of mature cortical pyramidal dendritic arbors after stroke.

Project description:The manner in which fully mature peri-infarct cortical dendritic arbors remodel after stroke, and thus may possibly contribute to stroke-induced changes in cortical receptive fields, is unknown. In this study, we used longitudinal in vivo two-photon imaging to investigate the extent to which brain ischemia can trigger dendritic remodeling of pyramidal neurons in the adult mouse somatosensory cortex, and to determine the nature by which remodeling proceeds over time and space. Before the induction of stroke, dendritic arbors were relatively stable over several weeks. However, after stroke, apical dendritic arbor remodeling increased significantly (dendritic tip growth and retraction), particularly within the first 2 weeks after stroke. Despite a threefold increase in structural remodeling, the net length of arbors did not change significantly over time because dendrite extensions away from the stroke were balanced by the shortening of tips near the infarct. Therefore, fully mature cortical pyramidal neurons retain the capacity for extensive structural plasticity and remodel in a balanced and branch-specific manner.

| S-EPMC2949167 | biostudies-literature

SAD kinases sculpt axonal arbors of sensory neurons through long- and short-term responses to neurotrophin signals.

Project description:Extrinsic cues activate intrinsic signaling mechanisms to pattern neuronal shape and connectivity. We showed previously that three cytoplasmic Ser/Thr kinases, LKB1, SAD-A, and SAD-B, control early axon-dendrite polarization in forebrain neurons. Here, we assess their role in other neuronal types. We found that all three kinases are dispensable for axon formation outside of the cortex but that SAD kinases are required for formation of central axonal arbors by subsets of sensory neurons. The requirement for SAD kinases is most prominent in NT-3 dependent neurons. SAD kinases transduce NT-3 signals in two ways through distinct pathways. First, sustained NT-3/TrkC signaling increases SAD protein levels. Second, short-duration NT-3/TrkC signals transiently activate SADs by inducing dephosphorylation of C-terminal domains, thereby allowing activating phosphorylation of the kinase domain. We propose that SAD kinases integrate long- and short-duration signals from extrinsic cues to sculpt axon arbors within the CNS.

| S-EPMC3725037 | biostudies-literature

Local Microtubule and F-Actin Distributions Fully Constrain the Spatial Geometry of <i>Drosophila</i> Sensory Dendritic Arbors.

Project description:Dendritic morphology underlies the source and processing of neuronal signal inputs. Morphology can be broadly described by two types of geometric characteristics. The first is dendrogram topology, defined by the length and frequency of the arbor branches; the second is spatial embedding, mainly determined by branch angles and straightness. We have previously demonstrated that microtubules and actin filaments are associated with arbor elongation and branching, fully constraining dendrogram topology. Here, we relate the local distribution of these two primary cytoskeletal components with dendritic spatial embedding. We first reconstruct and analyze 167 sensory neurons from the Drosophila larva encompassing multiple cell classes and genotypes. We observe that branches with a higher microtubule concentration tend to deviate less from the direction of their parent branch across all neuron types. Higher microtubule branches are also overall straighter. F-actin displays a similar effect on angular deviation and branch straightness, but not as consistently across all neuron types as microtubule. These observations raise the question as to whether the associations between cytoskeletal distributions and arbor geometry are sufficient constraints to reproduce type-specific dendritic architecture. Therefore, we create a computational model of dendritic morphology purely constrained by the cytoskeletal composition measured from real neurons. The model quantitatively captures both spatial embedding and dendrogram topology across all tested neuron groups. These results suggest a common developmental mechanism regulating diverse morphologies, where the local cytoskeletal distribution can fully specify the overall emergent geometry of dendritic arbors.

| S-EPMC10095360 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data