If you use EXTRACT for your own research, please consider citing these estimation of neural signals in calcium imaging},Īuthor='/data') In this option, there is no restriction on the filepath or the dataset names.Ĭonfig: a struct whose fields define the various parameters used for signal extraction (See Configurations for details on config). Its main features and the mathematical foundations behind EXTRACT as well as a comparison with state-of-the-art methods can be found in the papers cited below (Links to papers: Inan et al., 2021 and Inan et al., 2017). We also provide some links to the external repositories whenever needed (colored as orange in the figure right). EXTRACT code in this repository provides most of the pipeline (colored as green in the figure). Later, the processed movie is used by the EXTRACT algorithm to perform tractable and robust cell extraction, which puts out the temporal traces and spatial maps for future data analysis. Then, one performs motion correction and various pre-processing steps. The pipeline takes a raw 1p/2p Ca 2+ imaging movie as an input. For a trained person (feel free to schedule a tutorial for your lab!), this process usually takes around few minutes.ĮXTRACT can be thought of as being part of a signal extraction pipeline, as illustrated by the figure on the right. EXTRACT needs to be optimized per surgery/imaging modality type (practically once in the life-time of a study). 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. Please note that this is the raw output, with no post-processing and/or manual annotation/selection by users. We show an example output of EXTRACT on a low SNR movie, in the figure on the right donated by Dr. EXTRACT makes minimal assumptions about the data, which is the main reason behind its high robustness and superior performance.
Thank you!ĮXTRACT 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 Ca 2+ imaging movies. (Please be sure to add this email to your contact list so that replies and announcements do not go to your spam folder). 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 along with your name and institution. Thank you for your interest in EXTRACT, a cell extraction routine with native GPU implementation.
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