NETCAL: An interactive platform for large-scale, NETwork and population dynamics analysis of CALcium imaging recordings
Calcium imaging has become the preferred technique in neuroscience to simultaneously record the activity of thousands of cells. Yet most tools to analyze the recordings are rather rudimentary or require extensive knowledge of other disciplines, from machine learning to big data and network theory. Moreover, there is often a disconnection between the experiments and their analysis and outcome, usually taking place days apart and/or being done by different people.
We present NETCAL, a MATLAB-built, dedicated software platform to record, manage and analyze high-speed high-resolution calcium imaging experiments. Its ease of use, interactive graphical interface and exhaustive documentation is aimed to wet-lab researchers, but it will also meet the needs of any experienced data scientist through its plugin and scripting system. We have developed a large set of tools and incorporated state-of-the-art algorithms and toolboxes for large-scale analysis of network and population dynamics. Analyses include: automated cell detection (both static and dynamic); trace and population sorting through machine learning, clustering and pattern recognition; bursting dynamics; spike detection; network inference (from functional networks to causal relations); and many more. Several of these tools are also available in real-time, e.g. cells and spikes can be monitored during the actual recording, giving the researcher extensive feedback on the progress of the experiment.
We have tested and used the software in several different experimental preparations and laboratory equipment. For instance, NETCAL has been used to test the viability and performance of differentiation protocols from human induced pluripotent stem cells (hISPCs); to characterize the individual and collective behavior of dissociated cortical and striatal cultures from Huntington’s disease (HD) mouse models; to reveal the communication between neurons and astrocytes in rat hippocampal cultures; and to detect propagating activity patterns in cortical cultures. Although NETCAL has been developed for calcium recordings in cultures, we have successfully tested and used it in other preparations, e.g., in-vivo calcium imaging and multi-electrode arrays.
Our platform has been developed by scientists for scientists, to promote and foster the development of tools for the replication and validation of experimental results. The software is highly modular, and its implementation provides easy extendability to adapt it to the specific requirements of any research group.
- For now, you can cite the Zenodo repository: Javier G. Orlandi, Sara Fernández-García, Andrea Comella-Bolla, Mercè Masana, Gerardo García-Díaz Barriga, Mohammad Yaghoubi , Alexander Kipp, Josep M. Canals, Michael A. Colicos, Jörn Davidsen, Jordi Alberch and Jordi Soriano. (2017, November 12). NETCAL: An interactive platform for large-scale, NETwork and population dynamics analysis of CALcium imaging recordings (Version 7.0.0 Open Beta). Zenodo. 10.5281/zenodo.1119025
- Reference to the peer reviewed article will be coming soon.
- Please consider citing any of the reference papers if you use any of the relevant functions. The Help window on most NETCAL functions informs you about adequate references. Full list here
If you have any questions please contact Javier Orlandi at email@example.com
Copyright (c) 2017 Javier G. Orlandi
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the “Software”), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE