EXTRACT-public

Version 1.3.1 (3.23 MB) by Fatih Dinc
EXTRACT is a tractable and robust automated cell extraction tool for calcium imaging, which extracts the activities of cells as time series
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Updated 4 Oct 2024
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Cite As

EXTRACT is described in two accompanying papers: Dinc & Inan et al., 2024 (https://www.biorxiv.org/content/10.1101/2021.03.24.436279v3.abstract) and Inan et al., 2017 (https://pyramidal.stanford.edu/publications/Inan_NIPS_2017.pdf). Please cite these papers if you use EXTRACT in your own work.

MATLAB Release Compatibility
Created with R2019b
Compatible with any release
Platform Compatibility
Windows macOS Linux
Categories
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EXTRACT

EXTRACT/main_functions/debug_utils

EXTRACT/main_functions/debug_utils/brewermap

EXTRACT/main_functions/helper_functions

EXTRACT/main_functions/solvers/base solvers for multiple cells

EXTRACT/main_functions/solvers/cell finding solvers

EXTRACT/main_functions/solvers/cell refinement + frr solvers

EXTRACT/modules

EXTRACT/summary functions

External algorithms

External algorithms/Template scripts

External algorithms/parfor_progress

External algorithms/progressbar

External algorithms/simulation_utils

Learning-materials/Additional demos/NWB Demos

Learning-materials/Additional demos/Neurofinder_training_0200

Learning-materials/Additional demos/SVD-denoising for low SNR movies

Learning-materials/Additional demos/Simulating movies

Learning-materials/Lecture-Tutorials/Tutorial-1-Starting-code

Learning-materials/Lecture-Tutorials/Tutorial-2-Parallelization

Learning-materials/Lecture-Tutorials/Tutorial-3-Preprocessing

Learning-materials/Lecture-Tutorials/Tutorial-4-Cellfinding

Learning-materials/Lecture-Tutorials/Tutorial-5-Cell-refinement

Learning-materials/Lecture-Tutorials/Tutorial-6-Final-robust-regression

Learning-materials/Lecture-Tutorials/Tutorial-1-Starting-code

Learning-materials/Lecture-Tutorials/Tutorial-2-Parallelization

Learning-materials/Lecture-Tutorials/Tutorial-3-Preprocessing

Learning-materials/Lecture-Tutorials/Tutorial-4-Cellfinding

Learning-materials/Lecture-Tutorials/Tutorial-5-Cell-refinement

Learning-materials/Lecture-Tutorials/Tutorial-6-Final-robust-regression

Versions that use the GitHub default branch cannot be downloaded

Version Published Release Notes
1.3.1

See release notes for this release on GitHub: https://github.com/schnitzer-lab/EXTRACT-public/releases/tag/v1.3.1
1.3.0

See release notes for this release on GitHub: https://github.com/schnitzer-lab/EXTRACT-public/releases/tag/v1.3.0
1.0.0

See Github page
0.7.3

Proper citation added
0.7.2

To view or report issues in this GitHub add-on, visit the GitHub Repository.
To view or report issues in this GitHub add-on, visit the GitHub Repository.