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cytoNet: Spatiotemporal Network Analysis of Cell Communities

https://doi.org/10.1101/180273
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Variability and partial synchrony of the cell cycle in the germinal zone of the early embryonic cerebral cortex
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PySpacell: A Python Package for Spatial Analysis of Cell Images
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Visualizing Spatiotemporal Dynamics of Multicellular Cell-Cycle Progression
inferredcites →https://doi.org/10.1016/j.cell.2020.07.005openalex-snapshot
Coordinated Cellular Neighborhoods Orchestrate Antitumoral Immunity at the Colorectal Cancer Invasive Front
inferredcites →https://doi.org/10.1016/j.celrep.2018.05.062openalex-snapshot
MIN1PIPE: A Miniscope 1-Photon-Based Calcium Imaging Signal Extraction Pipeline
inferredcites →https://doi.org/10.1016/j.celrep.2020.107523openalex-snapshot
CytoMAP: A Spatial Analysis Toolbox Reveals Features of Myeloid Cell Organization in Lymphoid Tissues
inferredcites →https://doi.org/10.1016/j.cels.2018.09.001openalex-snapshot
Multivariate Control of Transcript to Protein Variability in Single Mammalian Cells
inferredcites →https://doi.org/10.1016/j.cels.2020.04.003openalex-snapshot
nucleAIzer: A Parameter-free Deep Learning Framework for Nucleus Segmentation Using Image Style Transfer
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Reported Prestroke Physical Activity Is Associated with Vascular Endothelial Growth Factor Expression and Good Outcomes after Stroke
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In vitro assays of angiogenesis for assessment of angiogenic and anti-angiogenic agents
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Oscillations in Notch Signaling Regulate Maintenance of Neural Progenitors
inferredcites →https://doi.org/10.1016/j.neuron.2013.12.011openalex-snapshot
Central Terminal Sensitization of TRPV1 by Descending Serotonergic Facilitation Modulates Chronic Pain
inferredcites →https://doi.org/10.1016/j.neuron.2016.07.044openalex-snapshot
Coupled Activation of Primary Sensory Neurons Contributes to Chronic Pain
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An Efficient and Reversible Transposable System for Gene Delivery and Lineage-Specific Differentiation in Human Embryonic Stem Cells
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2D and 3D Stem Cell Models of Primate Cortical Development Identify Species-Specific Differences in Progenitor Behavior Contributing to Brain Size
inferredcites →https://doi.org/10.1016/j.stem.2016.10.017openalex-snapshot
Zika Virus Disrupts Neural Progenitor Development and Leads to Microcephaly in Mice
inferredcites →https://doi.org/10.1021/acsnano.5b01366openalex-snapshot
Recapitulation and Modulation of the Cellular Architecture of a User-Chosen Cell of Interest Using Cell-Derived, Biomimetic Patterning
inferredcites →https://doi.org/10.1038/msb.2012.9openalex-snapshot
Single‐cell analysis of population context advances RNAi screening at multiple levels
inferredcites →https://doi.org/10.1038/nature08282openalex-snapshot
Population context determines cell-to-cell variability in endocytosis and virus infection
inferredcites →https://doi.org/10.1038/nbt.3722openalex-snapshot
Imagining the future of bioimage analysis
inferredcites →https://doi.org/10.1038/ncb3443openalex-snapshot
Asymmetric division coordinates collective cell migration in angiogenesis
inferredcites →https://doi.org/10.1038/nmeth.3545openalex-snapshot
Trajectories of cell-cycle progression from fixed cell populations
inferredcites →https://doi.org/10.1038/nmeth.4391openalex-snapshot
histoCAT: analysis of cell phenotypes and interactions in multiplex image cytometry data
inferredcites →https://doi.org/10.1038/nmeth.4634openalex-snapshot
Identification of spatial expression trends in single-cell gene expression data
inferredcites →https://doi.org/10.1038/nmeth.4636openalex-snapshot
SpatialDE: identification of spatially variable genes
inferredcites →https://doi.org/10.1038/nn.4502openalex-snapshot
Network neuroscience
inferredcites →https://doi.org/10.1038/nphys209openalex-snapshot
Detecting rich-club ordering in complex networks
inferredcites →https://doi.org/10.1038/nprot.2016.105openalex-snapshot
Cell Painting, a high-content image-based assay for morphological profiling using multiplexed fluorescent dyes
inferredcites →https://doi.org/10.1038/nrn2759openalex-snapshot
Mechanisms underlying spontaneous patterned activity in developing neural circuits
inferredcites →https://doi.org/10.1038/s41583-018-0038-8openalex-snapshot
On the nature and use of models in network neuroscience
inferredcites →https://doi.org/10.1038/s41586-019-1049-yopenalex-snapshot
Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+
inferredcites →https://doi.org/10.1038/s41592-019-0548-yopenalex-snapshot
High-definition spatial transcriptomics for in situ tissue profiling
inferredcites →https://doi.org/10.1038/s41592-019-0582-9openalex-snapshot
ilastik: interactive machine learning for (bio)image analysis
inferredcites →https://doi.org/10.1038/s41598-021-84828-zopenalex-snapshot
Integrins and extracellular matrix proteins modulate adipocyte thermogenic capacity
inferredcites →https://doi.org/10.1039/c5tb00952aopenalex-snapshot
Hydrogel-based engineering of beige adipose tissue
inferredcites →https://doi.org/10.1073/pnas.1220179110openalex-snapshot
Neural progenitors organize in small-world networks to promote cell proliferation
inferredcites →https://doi.org/10.1093/bioinformatics/bty281openalex-snapshot
CaSiAn: a Calcium Signaling Analyzer tool
inferredcites →https://doi.org/10.1101/061507openalex-snapshot
Suite2p: beyond 10,000 neurons with standard two-photon microscopy
inferredcites →https://doi.org/10.1101/190348openalex-snapshot
ABLE: an Activity-Based Level Set Segmentation Algorithm for Two-Photon Calcium Imaging Data
inferredcites →https://doi.org/10.1101/2020.02.13.20017921openalex-snapshot
The Tumor Profiler Study: Integrated, multi-omic, functional tumor profiling for clinical decision support
inferredcites →https://doi.org/10.1101/2021.01.25.427969openalex-snapshot
AI-driven Deep Visual Proteomics defines cell identity and heterogeneity
inferredcites →https://doi.org/10.1103/physreve.85.016117openalex-snapshot
Overview of metrics and their correlation patterns for multiple-metric topology analysis on heterogeneous graph ensembles
inferredcites →https://doi.org/10.1103/physrevlett.89.208701openalex-snapshot
Assortative Mixing in Networks
inferredcites →https://doi.org/10.1115/nemb2013-93124openalex-snapshot
Predicting Endothelial Cell Phenotypes in Angiogenesis
inferredcites →https://doi.org/10.1126/science.aal3321openalex-snapshot
A subcellular map of the human proteome
inferredcites →https://doi.org/10.1126/science.aar7042openalex-snapshot
Multiplexed protein maps link subcellular organization to cellular states
inferredcites →https://doi.org/10.1177/0271678x17702669openalex-snapshot
Neuroprotective and regenerative roles of intranasal Wnt-3a administration after focal ischemic stroke in mice
inferredcites →https://doi.org/10.1177/1176935119856595openalex-snapshot
Leveraging Image-Derived Phenotypic Measurements for Drug-Target Interaction Predictions
inferredcites →https://doi.org/10.1186/gb-2006-7-10-r100openalex-snapshot
CellProfiler: image analysis software for identifying and quantifying cell phenotypes
inferredcites →https://doi.org/10.1186/s12859-018-2022-8openalex-snapshot
Shrinkage Clustering: a fast and size-constrained clustering algorithm for biomedical applications
inferredcites →https://doi.org/10.1201/b18320-15openalex-snapshot
Computational Cell Phenotyping in the Lab, Plant, and Clinic
inferredcites →https://doi.org/10.1210/en.2017-00186openalex-snapshot
The Absence of Laminin α4 in Male Mice Results in Enhanced Energy Expenditure and Increased Beige Subcutaneous Adipose Tissue
inferredcites →https://doi.org/10.1214/18-aoas1159openalex-snapshot
SCALPEL: Extracting neurons from calcium imaging data
inferredcites →https://doi.org/10.1371/journal.pbio.2005970openalex-snapshot
CellProfiler 3.0: Next-generation image processing for biology
inferredcites →https://doi.org/10.1371/journal.pcbi.1005526openalex-snapshot
An integrated calcium imaging processing toolbox for the analysis of neuronal population dynamics
inferredcites →https://doi.org/10.1371/journal.pcbi.1006054openalex-snapshot
An open source tool for automatic spatiotemporal assessment of calcium transients and local ‘signal-close-to-noise’ activity in calcium imaging data
inferredcites →https://doi.org/10.1371/journal.pone.0109854openalex-snapshot
Laminin α4 Deficient Mice Exhibit Decreased Capacity for Adipose Tissue Expansion and Weight Gain
inferredcites →https://doi.org/10.1523/jneurosci.17-06-02088.1997openalex-snapshot
Synchrony of Clonal Cell Proliferation and Contiguity of Clonally Related Cells: Production of Mosaicism in the Ventricular Zone of Developing Mouse Neocortex
inferredcites →https://doi.org/10.1523/jneurosci.2663-18.2019openalex-snapshot
Differences between Dorsal Root and Trigeminal Ganglion Nociceptors in Mice Revealed by Translational Profiling
inferredcites →https://doi.org/10.3389/fncir.2014.00111openalex-snapshot
Network analysis of time-lapse microscopy recordings
inferredcites →https://doi.org/10.3389/fninf.2014.00080openalex-snapshot
SIMA: Python software for analysis of dynamic fluorescence imaging data
inferredcites →https://doi.org/10.3389/fninf.2017.00044openalex-snapshot
SamuROI, a Python-Based Software Tool for Visualization and Analysis of Dynamic Time Series Imaging at Multiple Spatial Scales
inferredcites →https://doi.org/10.3389/fnins.2018.00958openalex-snapshot
CAVE: An Open-Source Tool for Combined Analysis of Head-Mounted Calcium Imaging and Behavior in MATLAB
inferredcites →https://doi.org/10.3390/bioengineering7030114openalex-snapshot
Optimization of Co-Culture Conditions for a Human Vascularized Adipose Tissue Model
inferredcites →https://doi.org/10.7554/elife.28728openalex-snapshot
Efficient and accurate extraction of in vivo calcium signals from microendoscopic video data
inferredcites →https://doi.org/10.7554/elife.38173openalex-snapshot
CaImAn an open source tool for scalable calcium imaging data analysis

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inferred← citeshttps://doi.org/10.1016/j.celrep.2020.107523openalex-snapshot
CytoMAP: A Spatial Analysis Toolbox Reveals Features of Myeloid Cell Organization in Lymphoid Tissues
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