EXTRACT-public

Version 1.0.0 (18.8 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 26 Jul 2024
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EXTRACT

Introduction

Example_movie

EXTRACT is a tractable and robust automated cell extraction tool for calcium imaging, which extracts the activities of cells as time series from both one-photon and two-photon Ca2+ imaging movies. EXTRACT makes minimal assumptions about the data, which is the main reason behind its high robustness and superior performance.

We show an example output of EXTRACT on a low SNR movie, in the figure on the right donated by Dr. Peng Yuan. Please note that this is the raw output, with no post-processing and/or manual annotation/selection by users. This run is a result of a batch processing of >30 sessions, optimized only once at the beginning of the study, with no extra parameter tweaking particular to this session. EXTRACT needs to be optimized per surgery/imaging modality type (practically once in the life-time of a study). For a trained person (feel free to schedule a tutorial for your lab!), this process usually takes around few minutes.

Installation

Use the Add-on Explorer and search for EXTRACT (recommended), or install files from this GitHub repo.

Getting Started

Browse the tutorial examples to quickly gain expertise with EXTRACT. You can view the tutorials 👀 or run▶️ most of the tutorials on MATLAB Online. Or work any of the tutorials on your own computer.

<markdown-accessiblity-table><table class="readme_table"> <thead> <tr> <th class="readme_th">Tutorial</th> <th class="readme_th">View</th> <th class="readme_th">Run</th> </tr> </thead> <tbody> <tr> <td class="readme_td">1 - Starting Code</td> <td class="readme_td"><a href="https://viewer.mathworks.com/?viewer=live_code&amp;url=https%3A%2F%2Fwww.mathworks.com%2Fmatlabcentral%2Fmlc-downloads%2Fdownloads%2F6d2fb9fc-2974-4fac-9eb3-83340b9f5095%2F1721947761%2Ffiles%2FLearning%20materials%2FLecture%20Tutorials%2FTutorial%201%20-%20Starting%20code%2Ftutorial_1.mlx&amp;embed=web" rel="nofollow noopener noreferrer" target="_blank" rel="nofollow noopener noreferrer">👀</a></td> <td class="readme_td"><a href="https://matlab.mathworks.com/open/github/v1?repo=schnitzer-lab/EXTRACT-public&amp;file=Lecture%20Tutorials/Tutorial%201%20-%20Cell%20refinement/tutorial_1.mlx" rel="nofollow noopener noreferrer" target="_blank" rel="nofollow noopener noreferrer"><img src="https://camo.githubusercontent.com/5047ced9e66f50cb2335e23dcd3242f1ae88a35ab5a32a32ef51d0298f784617/68747470733a2f2f7777772e6d617468776f726b732e636f6d2f696d616765732f726573706f6e736976652f676c6f62616c2f6f70656e2d696e2d6d61746c61622d6f6e6c696e652e737667" alt="Open in MATLAB Online" data-canonical-src="https://www.mathworks.com/images/responsive/global/open-in-matlab-online.svg" style="max-width: 100%;"></a></td> </tr> <tr> <td class="readme_td">2 - Parallelization</td> <td class="readme_td"><a href="https://viewer.mathworks.com/?viewer=live_code&amp;url=https%3A%2F%2Fwww.mathworks.com%2Fmatlabcentral%2Fmlc-downloads%2Fdownloads%2F6d2fb9fc-2974-4fac-9eb3-83340b9f5095%2F1721947761%2Ffiles%2FLearning%20materials%2FLecture%20Tutorials%2FTutorial%202%20-%20Parallelization%2Ftutorial_2.mlx&amp;embed=web" rel="nofollow noopener noreferrer" target="_blank" rel="nofollow noopener noreferrer">👀</a></td> <td class="readme_td"><a href="https://matlab.mathworks.com/open/github/v1?repo=schnitzer-lab/EXTRACT-public&amp;file=Lecture%20Tutorials/Tutorial%202%20-%20Cell%20refinement/tutorial_2.mlx" rel="nofollow noopener noreferrer" target="_blank" rel="nofollow noopener noreferrer"><img src="https://camo.githubusercontent.com/5047ced9e66f50cb2335e23dcd3242f1ae88a35ab5a32a32ef51d0298f784617/68747470733a2f2f7777772e6d617468776f726b732e636f6d2f696d616765732f726573706f6e736976652f676c6f62616c2f6f70656e2d696e2d6d61746c61622d6f6e6c696e652e737667" alt="Open in MATLAB Online" data-canonical-src="https://www.mathworks.com/images/responsive/global/open-in-matlab-online.svg" style="max-width: 100%;"></a></td> </tr> <tr> <td class="readme_td">3 - Preprocessing</td> <td class="readme_td"><a href="https://viewer.mathworks.com/?viewer=live_code&amp;url=https%3A%2F%2Fwww.mathworks.com%2Fmatlabcentral%2Fmlc-downloads%2Fdownloads%2F6d2fb9fc-2974-4fac-9eb3-83340b9f5095%2F1721947761%2Ffiles%2FLearning%20materials%2FLecture%20Tutorials%2FTutorial%203%20-%20Preprocessing%2Ftutorial_3.mlx&amp;embed=web" rel="nofollow noopener noreferrer" target="_blank" rel="nofollow noopener noreferrer">👀</a></td> <td class="readme_td"><a href="https://matlab.mathworks.com/open/github/v1?repo=schnitzer-lab/EXTRACT-public&amp;file=Lecture%20Tutorials/Tutorial%203%20-%20Preprocessing/tutorial_3.mlx" rel="nofollow noopener noreferrer" target="_blank" rel="nofollow noopener noreferrer"><img src="https://camo.githubusercontent.com/5047ced9e66f50cb2335e23dcd3242f1ae88a35ab5a32a32ef51d0298f784617/68747470733a2f2f7777772e6d617468776f726b732e636f6d2f696d616765732f726573706f6e736976652f676c6f62616c2f6f70656e2d696e2d6d61746c61622d6f6e6c696e652e737667" alt="Open in MATLAB Online" data-canonical-src="https://www.mathworks.com/images/responsive/global/open-in-matlab-online.svg" style="max-width: 100%;"></a></td> </tr> <tr> <td class="readme_td">4 - Cellfinding</td> <td class="readme_td"><a href="https://viewer.mathworks.com/?viewer=live_code&amp;url=https%3A%2F%2Fwww.mathworks.com%2Fmatlabcentral%2Fmlc-downloads%2Fdownloads%2F6d2fb9fc-2974-4fac-9eb3-83340b9f5095%2F1721947761%2Ffiles%2FLearning%20materials%2FLecture%20Tutorials%2FTutorial%204%20-%20Cellfinding%2Ftutorial_4.mlx&amp;embed=web" rel="nofollow noopener noreferrer" target="_blank" rel="nofollow noopener noreferrer">👀</a></td> <td class="readme_td"><a href="https://matlab.mathworks.com/open/github/v1?repo=schnitzer-lab/EXTRACT-public&amp;file=Lecture%20Tutorials/Tutorial%204%20-%20Cell%20finding/tutorial_4.mlx" rel="nofollow noopener noreferrer" target="_blank" rel="nofollow noopener noreferrer"><img src="https://camo.githubusercontent.com/5047ced9e66f50cb2335e23dcd3242f1ae88a35ab5a32a32ef51d0298f784617/68747470733a2f2f7777772e6d617468776f726b732e636f6d2f696d616765732f726573706f6e736976652f676c6f62616c2f6f70656e2d696e2d6d61746c61622d6f6e6c696e652e737667" alt="Open in MATLAB Online" data-canonical-src="https://www.mathworks.com/images/responsive/global/open-in-matlab-online.svg" style="max-width: 100%;"></a></td> </tr> <tr> <td class="readme_td">5 - Cell refinement</td> <td class="readme_td"><a href="https://viewer.mathworks.com/?viewer=live_code&amp;url=https%3A%2F%2Fwww.mathworks.com%2Fmatlabcentral%2Fmlc-downloads%2Fdownloads%2F6d2fb9fc-2974-4fac-9eb3-83340b9f5095%2F1721947761%2Ffiles%2FLearning%20materials%2FLecture%20Tutorials%2FTutorial%205%20-%20Cell%20refinement%2Ftutorial_5.mlx&amp;embed=web" rel="nofollow noopener noreferrer" target="_blank" rel="nofollow noopener noreferrer">👀</a></td> <td class="readme_td"><a href="https://matlab.mathworks.com/open/github/v1?repo=schnitzer-lab/EXTRACT-public&amp;file=Lecture%20Tutorials/Tutorial%205%20-%20Cell%20refinement/tutorial_5.mlx" rel="nofollow noopener noreferrer" target="_blank" rel="nofollow noopener noreferrer"><img src="https://camo.githubusercontent.com/5047ced9e66f50cb2335e23dcd3242f1ae88a35ab5a32a32ef51d0298f784617/68747470733a2f2f7777772e6d617468776f726b732e636f6d2f696d616765732f726573706f6e736976652f676c6f62616c2f6f70656e2d696e2d6d61746c61622d6f6e6c696e652e737667" alt="Open in MATLAB Online" data-canonical-src="https://www.mathworks.com/images/responsive/global/open-in-matlab-online.svg" style="max-width: 100%;"></a></td> </tr> <tr> <td class="readme_td">6 - Final robust regression</td> <td class="readme_td"><a href="https://viewer.mathworks.com/?viewer=live_code&amp;url=https%3A%2F%2Fwww.mathworks.com%2Fmatlabcentral%2Fmlc-downloads%2Fdownloads%2F6d2fb9fc-2974-4fac-9eb3-83340b9f5095%2F1721947761%2Ffiles%2FLearning%20materials%2FLecture%20Tutorials%2FTutorial%206%20-%20Final%20robust%20regression%2Ftutorial_6.mlx&amp;embed=web" rel="nofollow noopener noreferrer" target="_blank" rel="nofollow noopener noreferrer">👀</a></td> <td class="readme_td"><a href="https://matlab.mathworks.com/open/github/v1?repo=schnitzer-lab/EXTRACT-public&amp;file=Lecture%20Tutorials/Tutorial%206%20-%20Cell%20refinement/tutorial_6.mlx" rel="nofollow noopener noreferrer" target="_blank" rel="nofollow noopener noreferrer"><img src="https://camo.githubusercontent.com/5047ced9e66f50cb2335e23dcd3242f1ae88a35ab5a32a32ef51d0298f784617/68747470733a2f2f7777772e6d617468776f726b732e636f6d2f696d616765732f726573706f6e736976652f676c6f62616c2f6f70656e2d696e2d6d61746c61622d6f6e6c696e652e737667" alt="Open in MATLAB Online" data-canonical-src="https://www.mathworks.com/images/responsive/global/open-in-matlab-online.svg" style="max-width: 100%;"></a></td> </tr> </tbody> </table></markdown-accessiblity-table>

The user manual

Please see the user manual inside the "Learning materials" folder. The user manual has a quick start guide, accompanied with several tutorials. The user manual also has several key insights for increasing the quality of cell extraction.

Instructional video

You can watch our 10-minute video about EXTRACT: Instructional video

Schedule a tutorial session!

Thank you for your interest in EXTRACT, a cell extraction routine with native GPU implementation. To receive occasional updates about new releases, to ask questions about EXTRACT usage, or schedule a tutorial session for your lab, please send an email to extractneurons@gmail.com along with your name and institution. (Please be sure to add this email to your contact list so that replies and announcements do not go to your spam folder). Thank you!

Questions

EXTRACT code is primarily written by Dr. Hakan Inan and Fatih Dinc in collaboration with many researchers in Schnitzerlab. The database is maintained by the current members of Schnitzerlab. If you have any questions or comments, please open an issue or contact via email extractneurons@gmail.com.

Citations

EXTRACT is described in two accompanying papers: Inan et al., 2021 and Inan et al., 2017. Please cite us if you use EXTRACT in your own work.

Cite As

Inan, Hakan, et al. Fast and Statistically Robust Cell Extraction from Large-Scale Neural Calcium Imaging Datasets. Cold Spring Harbor Laboratory, Mar. 2021, doi:10.1101/2021.03.24.436279.

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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
1.0.0

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.