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Automated cellular structure extraction in biological images with applications to calcium imaging data

https://doi.org/10.1101/313981
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What this work says

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

inferredcites →https://doi.org/10.1016/j.acha.2006.04.006openalex-snapshot
Diffusion maps
inferredcites →https://doi.org/10.1016/j.acha.2013.05.002openalex-snapshot
Texture separation via a reference set
inferredcites →https://doi.org/10.1016/j.acha.2015.06.008openalex-snapshot
Parsimonious representation of nonlinear dynamical systems through manifold learning: A chemotaxis case study
inferredcites →https://doi.org/10.1016/j.acha.2018.04.001openalex-snapshot
On the diffusion geometry of graph Laplacians and applications
inferredcites →https://doi.org/10.1016/j.jnt.2017.09.021openalex-snapshot
The geometry of nodal sets and outlier detection
inferredcites →https://doi.org/10.1016/j.neunet.2014.03.007openalex-snapshot
Detecting cells using non-negative matrix factorization on calcium imaging data
inferredcites →https://doi.org/10.1016/j.neuron.2009.08.009openalex-snapshot
Automated Analysis of Cellular Signals from Large-Scale Calcium Imaging Data
inferredcites →https://doi.org/10.1016/j.neuron.2015.11.037openalex-snapshot
Simultaneous Denoising, Deconvolution, and Demixing of Calcium Imaging Data
inferredcites →https://doi.org/10.1016/j.neuron.2018.05.015openalex-snapshot
Unsupervised Discovery of Demixed, Low-Dimensional Neural Dynamics across Multiple Timescales through Tensor Component Analysis
inferredcites →https://doi.org/10.1038/nm.3488openalex-snapshot
Multiplexed ion beam imaging of human breast tumors
inferredcites →https://doi.org/10.1038/nmeth.1453openalex-snapshot
High-speed in vivo calcium imaging reveals neuronal network activity with near-millisecond precision
inferredcites →https://doi.org/10.1038/nmeth.2869openalex-snapshot
Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry
inferredcites →https://doi.org/10.1038/nn.2620openalex-snapshot
Parallel processing of visual space by neighboring neurons in mouse visual cortex
inferredcites →https://doi.org/10.1038/nrn3469openalex-snapshot
Corticostriatal connectivity and its role in disease
inferredcites →https://doi.org/10.1073/pnas.1107769108openalex-snapshot
Randomized approximate nearest neighbors algorithm
inferredcites →https://doi.org/10.1088/1741-2560/10/4/046017openalex-snapshot
A finite rate of innovation algorithm for fast and accurate spike detection from two-photon calcium imaging
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/10.1109/34.868688openalex-snapshot
Normalized cuts and image segmentation
inferredcites →https://doi.org/10.1109/jstsp.2016.2602061openalex-snapshot
Hierarchical Coupled-Geometry Analysis for Neuronal Structure and Activity Pattern Discovery
inferredcites →https://doi.org/10.1109/tasl.2012.2205243openalex-snapshot
Supervised Graph-Based Processing for Sequential Transient Interference Suppression
inferredcites →https://doi.org/10.1109/tgrs.2014.2364333openalex-snapshot
Graph-Based Supervised Automatic Target Detection
inferredcites →https://doi.org/10.1137/070712146openalex-snapshot
Diffusion Interpretation of Nonlocal Neighborhood Filters for Signal Denoising
inferredcites →https://doi.org/10.1145/3004053openalex-snapshot
Algorithm 971
inferredcites →https://doi.org/10.1152/jn.01073.2009openalex-snapshot
Fast Nonnegative Deconvolution for Spike Train Inference From Population Calcium Imaging
inferredcites →https://doi.org/10.1162/089976603321780317openalex-snapshot
Laplacian Eigenmaps for Dimensionality Reduction and Data Representation
inferredcites →https://doi.org/10.1214/14-aos1283openalex-snapshot
The geometry of kernelized spectral clustering
inferredcites →https://doi.org/10.21236/ada555156openalex-snapshot
A Randomized Approximate Nearest Neighbors Algorithm
inferredcites →https://doi.org/10.2174/1874241601104010010openalex-snapshot
Generating Evidence Based Interpretation of Hematology Screens via Anomaly Characterization
inferredcites →https://doi.org/10.48550/arxiv.1609.08251openalex-snapshot
Robust and efficient multi-way spectral clustering
inferredcites →https://doi.org/10.7551/mitpress/7503.003.0132openalex-snapshot
Fundamental Limitations of Spectral Clustering

What points at this work

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

inferred← citeshttps://doi.org/10.1016/b978-0-323-85796-3.00014-7openalex-snapshot
Machine learning data processing as a bridge between microscopy and the brain
inferred← citeshttps://doi.org/10.1016/j.conb.2018.11.004openalex-snapshot
Analysis pipelines for calcium imaging data
inferred← citeshttps://doi.org/10.1016/j.conb.2022.102627openalex-snapshot
Spatiotemporal dynamics in large-scale cortical networks
inferred← citeshttps://doi.org/10.1016/j.crmeth.2022.100299openalex-snapshot
SpecSeg is a versatile toolbox that segments neurons and neurites in chronic calcium imaging datasets based on low-frequency cross-spectral power
inferred← citeshttps://doi.org/10.1016/j.jneumeth.2021.109173openalex-snapshot
Neural anatomy and optical microscopy (NAOMi) simulation for evaluating calcium imaging methods
inferred← citeshttps://doi.org/10.1016/j.neuron.2020.09.031openalex-snapshot
Mesoscopic Imaging: Shining a Wide Light on Large-Scale Neural Dynamics
inferred← citeshttps://doi.org/10.1038/s41592-022-01422-5openalex-snapshot
Detecting and correcting false transients in calcium imaging
inferred← citeshttps://doi.org/10.1038/s41592-023-02098-1openalex-snapshot
The Cousa objective: a long-working distance air objective for multiphoton imaging in vivo
inferred← citeshttps://doi.org/10.1038/s41593-023-01498-yopenalex-snapshot
Rapid fluctuations in functional connectivity of cortical networks encode spontaneous behavior
inferred← citeshttps://doi.org/10.1093/imamat/hxy065openalex-snapshot
Manifold learning with bi-stochastic kernels
inferred← citeshttps://doi.org/10.1101/2021.08.15.456390openalex-snapshot
Rapid fluctuations in functional connectivity of cortical networks encode spontaneous
inferred← citeshttps://doi.org/10.1101/2025.04.15.648462openalex-snapshot
Fast and accessible morphology-free functional fluorescence imaging analysis
inferred← citeshttps://doi.org/10.1101/334706openalex-snapshot
Penalized matrix decomposition for denoising, compression, and improved demixing of functional imaging data
inferred← citeshttps://doi.org/10.1101/473470openalex-snapshot
Detecting and Correcting False Transients in Calcium Imaging
inferred← citeshttps://doi.org/10.1109/icassp.2019.8683375openalex-snapshot
Learning Spatially-correlated Temporal Dictionaries for Calcium Imaging
inferred← citeshttps://doi.org/10.1109/tip.2022.3171414openalex-snapshot
GraFT: Graph Filtered Temporal Dictionary Learning for Functional Neural Imaging
inferred← citeshttps://doi.org/10.1117/1.nph.9.4.041402openalex-snapshot
Review of data processing of functional optical microscopy for neuroscience
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1014038openalex-snapshot
Fast and accessible morphology-free functional fluorescence imaging analysis
inferred← citeshttps://doi.org/10.48550/arxiv.1807.06203openalex-snapshot
Penalized matrix decomposition for denoising, compression, and improved demixing of functional imaging data
inferred← citeshttps://doi.org/10.48550/arxiv.1910.04201openalex-snapshot
Randomized mixed Hölder function approximation in higher-dimensions
inferred← citeshttps://doi.org/10.64898/2026.08.07.743580openalex-snapshot
GIAnT: a Glutamate Imaging Analysis Toolbox
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