Software Open Access
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; Jordi Soriano
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.