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SimCalc simulates calcium imaging data, with the option for different neural shapes and locations
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README.rst

SimCalc

SimCalc (Simulated Calcium) simulates calcium imaging data, with the option for different neural shapes and locations.

This code was used for testing our FISSA toolbox, for more information see the FISSA repository and companion paper. For a detailed mathematical description of what SimCalc does see the FISSA methods.

Currently this code can be quite memory heavy, so on standard laptops it's best not to define too big field-of-views. For reference, a 100x100 pixel view with 3000 frames would use about 800MB, but this quickly goes up with larger field of views.

Installation

After downloading this repository, use a terminal to navigate into the base folder. Then:

pip install -e ./

Optionally, it is possible to install with all plotting requirements to run the example notebooks yourself:

pip install -e ./['plotting']

Usage

A general tutorial on the use of SimCalc can be found at: https://rochefort-lab.github.io/SimCalc/examples/Simulated_data_tutorial.html

The corresponding jupyter notebook can be found in the examples folder of this repository.

Citing SimCalc

If you use SimCalc for your research, please cite the following paper in any resulting publications:

S. W. Keemink, S. C. Lowe, J. M. P. Pakan, E. Dylda, M. C. W. van Rossum, and N. L. Rochefort. FISSA: A neuropil decontamination toolbox for calcium imaging signals, Scientific Reports, 8(1):3493, 2018. DOI:10.1038/s41598-018-21640-2.

For your convenience, the FISSA package ships with a copy of this citation in bibtex format, available at citation.bib.

License

Unless otherwise stated in individual files, all code is Copyright (c) 2015, Sander Keemink, Scott Lowe, and Nathalie Rochefort. All rights reserved.

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.

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