BlueRecording: A pipeline for the efficient calculation of extracellular recordings in large-scale neural circuit models

As the size and complexity of network simulations accessible to computational neuroscience grows, new avenues open for research into extracellularly recorded electric signals. Biophysically detailed simulations permit the identification of the biological origins of the different components of recorded signals, the evaluation of signal sensitivity to different anatomical, physiological, and geometric factors, and selection of recording parameters to maximize the signal information content. Simultaneously, virtual extracellular signals produced by these networks may become important metrics for neuro-simulation validation. To enable efficient calculation of extracellular signals from large neural network simulations, we have developed BlueRecording, a pipeline consisting of standalone Python code, along with extensions to the Neurodamus simulation control application, the CoreNEURON computation engine, and the SONATA data format, to permit online calculation of such signals. In particular, we implement a general form of the reciprocity theorem, which is capable of handling non-dipolar current sources, such as may be found in long axons and recordings close to the current source, as well as complex tissue anatomy, dielectric heterogeneity, and electrode geometries. To our knowledge, this is the first application of this generalized (i.e., non-dipolar) reciprocity-based approach to simulate EEG recordings. We use these tools to calculate extracellular signals from an in silico model of the rat somatosensory cortex and hippocampus and to study signal contribution differences between regions and cell types.Author summary: In this paper, we introduce BlueRecording, a suite of software tools that enables the simulation of extracellular recordings from large-scale neural circuit models. With BlueRecording, users can simulate EEG, ECoG, and intracellular recordings, using a variety of signal estimation methods. Notably, BlueRecording implements the innovative “generalized reciprocity approach”, which allows the accurate calculation of signals with arbitrarily complex electrode shapes and arrangements and heterogeneous, anisotropic head models. BlueRecording is tightly integrated into the CoreNEURON simulation engine, leading to a 3-fold improvement in computation time compared to the state-of-the-art. It is compatible with the SONATA format for neural circuit models; as demonstrators, we compute signals from in silico models of the rat somatosensory cortex and of the hippocampus using BlueRecording, which permits us to disambiguate the contributions of different cell types to the EEG signal.