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.
It is fairly straightforward to install EXTRACT. Simply download all the files from the repository and include them in the MATLAB path. Installation is complete.
Please note that EXTRACT makes use of various packages and toolboxes:
- Bioinformatics Toolbox
- Econometrics Toolbox
- Image Processing Toolbox
- Parallel Computing Toolbox
- Signal Processing Toolbox
- Statistics and Machine Learning Toolbox
- Wavelet Toolbox
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.
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!
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.
If you use EXTRACT for your own research, please cite the following works:
@article{inan2021fast,
author = {Inan, Hakan and Schmuckermair, Claudia and Tasci, Tugce and Ahanonu,
Biafra and Hernandez, Oscar and Lecoq, Jerome and Dinc, Fatih and Wagner,
Mark J and Erdogdu, Murat and Schnitzer, Mark J},
title = {Fast and statistically robust cell extraction from
large-scale neural calcium imaging datasets},
elocation-id = {2021.03.24.436279},
year = {2021},
doi = {10.1101/2021.03.24.436279},
URL = {https://www.biorxiv.org/content/early/2021/03/25/2021.03.24.436279},
eprint = {https://www.biorxiv.org/content/early/2021/03/25/2021.03.24.436279.full.pdf},
journal = {bioRxiv}
}
@article{inan2017robust,
title={Robust estimation of neural signals in calcium imaging},
author={Inan, Hakan and Erdogdu, Murat A and Schnitzer, Mark},
journal={Advances in neural information processing systems},
volume={30},
pages={2901--2910},
year={2017}
}Links to accompanying papers: Inan et al., 2021 and Inan et al., 2017.
Copyright (C) 2020 Schnitzerlab
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