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GAMer 2: A System for 3D Mesh Processing of Cellular Electron Micrographs

https://doi.org/10.1101/534479
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What this work says

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

inferredcites →https://doi.org/10.1006/jsbi.1996.0013openalex-snapshot
Computer Visualization of Three-Dimensional Image Data Using IMOD
inferredcites →https://doi.org/10.1007/978-3-642-21227-7_51openalex-snapshot
Representing Local Structure Using Tensors II
inferredcites →https://doi.org/10.1007/978-3-642-59195-2openalex-snapshot
Visualization and mathematics: experiments, simulations and environments
inferredcites →https://doi.org/10.1016/j.bpj.2019.10.004openalex-snapshot
Geometric Control of Frequency Modulation of cAMP Oscillations due to Calcium in Dendritic Spines
inferredcites →https://doi.org/10.1016/j.cagd.2005.04.003openalex-snapshot
A sharpness dependent filter for mesh smoothing
inferredcites →https://doi.org/10.1016/j.cell.2008.04.025openalex-snapshot
Cell Shape and Negative Links in Regulatory Motifs Together Control Spatial Information Flow in Signaling Networks
inferredcites →https://doi.org/10.1016/j.cell.2010.11.007openalex-snapshot
Mechanisms Determining the Morphology of the Peripheral ER
inferredcites →https://doi.org/10.1016/j.cell.2013.06.031openalex-snapshot
Stacked Endoplasmic Reticulum Sheets Are Connected by Helicoidal Membrane Motifs
inferredcites →https://doi.org/10.1016/j.cell.2013.06.032openalex-snapshot
Differential Geometry Meets the Cell
inferredcites →https://doi.org/10.1016/j.cell.2013.08.026openalex-snapshot
Decoding Information in Cell Shape
inferredcites →https://doi.org/10.1016/j.conb.2007.04.003openalex-snapshot
Ca2+ signaling in dendritic spines
inferredcites →https://doi.org/10.1016/j.finel.2008.03.004openalex-snapshot
High-fidelity geometric modeling for biomedical applications
inferredcites →https://doi.org/10.1016/j.jmgm.2008.01.007openalex-snapshot
Feature-preserving adaptive mesh generation for molecular shape modeling and simulation
inferredcites →https://doi.org/10.1016/j.jsb.2003.09.010openalex-snapshot
An improved algorithm for anisotropic nonlinear diffusion for denoising cryo-tomograms
inferredcites →https://doi.org/10.1016/j.micron.2014.01.009openalex-snapshot
Exploring the third dimension: Volume electron microscopy comes of age
inferredcites →https://doi.org/10.1016/s0959-4388(00)00218-xopenalex-snapshot
Ca2+ signaling in dendritic spines
inferredcites →https://doi.org/10.1038/s41598-019-48028-0openalex-snapshot
Geometric principles of second messenger dynamics in dendritic spines
inferredcites →https://doi.org/10.1073/pnas.1419997111openalex-snapshot
A model for the generation and interconversion of ER morphologies
inferredcites →https://doi.org/10.1073/pnas.1701078114openalex-snapshot
Contacts between the endoplasmic reticulum and other membranes in neurons
inferredcites →https://doi.org/10.1085/jgp.201812261openalex-snapshot
Dendritic spine geometry and spine apparatus organization govern the spatiotemporal dynamics of calcium
inferredcites →https://doi.org/10.1101/161950openalex-snapshot
Cell shape regulates subcellular organelle location to control early Ca 2+ signal dynamics in Vascular Smooth Muscle Cells
inferredcites →https://doi.org/10.1101/521740openalex-snapshot
Computational modeling reveals frequency modulation of calcium-cAMP/PKA pathway in dendritic spines
inferredcites →https://doi.org/10.1109/34.56205openalex-snapshot
Scale-space and edge detection using anisotropic diffusion
inferredcites →https://doi.org/10.1109/cvpr.2004.1315062openalex-snapshot
A segmentation-free approach for skeletonization of gray-scale images via anisotropic vector diffusion
inferredcites →https://doi.org/10.1111/boc.201600024openalex-snapshot
Volume scanning electron microscopy for imaging biological ultrastructure
inferredcites →https://doi.org/10.1111/jmi.12377openalex-snapshot
Reporting methods for processing and analysis of data from serial block face scanning electron microscopy
inferredcites →https://doi.org/10.1126/science.1114816openalex-snapshot
Neuronal Activity Regulates Diffusion Across the Neck of Dendritic Spines
inferredcites →https://doi.org/10.1126/science.aaf3928openalex-snapshot
Increased spatiotemporal resolution reveals highly dynamic dense tubular matrices in the peripheral ER
inferredcites →https://doi.org/10.1145/218380.218473openalex-snapshot
A signal processing approach to fair surface design
inferredcites →https://doi.org/10.1145/2629697openalex-snapshot
TetGen, a Delaunay-Based Quality Tetrahedral Mesh Generator
inferredcites →https://doi.org/10.1145/311535.311576openalex-snapshot
Implicit fairing of irregular meshes using diffusion and curvature flow
inferredcites →https://doi.org/10.11588/ans.2015.100.20553openalex-snapshot
The FEniCS Project Version 1.5
inferredcites →https://doi.org/10.1201/9781420044157.ch9openalex-snapshot
NMDA Receptor-Mediated Calcium Transients in Dendritic Spines
inferredcites →https://doi.org/10.1371/journal.pbio.1000190openalex-snapshot
Biphasic Synaptic Ca Influx Arising from Compartmentalized Electrical Signals in Dendritic Spines
inferredcites →https://doi.org/10.3791/51673openalex-snapshot
From Voxels to Knowledge: A Practical Guide to the Segmentation of Complex Electron Microscopy 3D-Data
inferredcites →https://doi.org/10.5281/zenodo.16444openalex-snapshot
A Tensor Approach For Local Structure Analysis In Multi-Dimensional Images

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1016/j.actbio.2019.06.003openalex-snapshot
Emerging themes and unifying concepts underlying cell behavior regulation by the pericellular space
inferred← citeshttps://doi.org/10.1016/j.bpj.2019.11.3400openalex-snapshot
An Open-Source Mesh Generation Platform for Biophysical Modeling Using Realistic Cellular Geometries
inferred← citeshttps://doi.org/10.1016/j.mineng.2025.109519openalex-snapshot
An experimental and computational study of the role of cytochrome 2 in the adhesion of Acidithiobacillus ferrooxidans to pyrite in fresh and saline water
inferred← citeshttps://doi.org/10.1016/j.sbi.2020.01.014openalex-snapshot
Multiscale simulation approaches to modeling drug–protein binding
inferred← citeshttps://doi.org/10.1085/jgp.201812261openalex-snapshot
Dendritic spine geometry and spine apparatus organization govern the spatiotemporal dynamics of calcium
inferred← citeshttps://doi.org/10.3389/fphy.2019.00247openalex-snapshot
Applications and Challenges of Machine Learning to Enable Realistic Cellular Simulations
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