realSEUDO for real-time calcium imaging analysis

Closed-loop neuroscience experimentation, where recorded neural activity is used to modify the experiment on-the-fly, is critical for deducing causal connections and optimizing experimental time. A critical step in creating a closed-loop experiment is real-time inference of neural activity from streaming recordings. One challenging modality for real-time processing is multi-photon calcium imaging (CI). CI enables the recording of activity in large populations of neurons however, often requires batch processing of the video data to extract single-neuron activity from the fluorescence videos. We use the recently proposed robust time-trace estimator--Sparse Emulation of Unused Dictionary Objects (SEUDO) algorithm--as a basis for a new on-line processing algorithm that simultaneously identifies neurons in the fluorescence video and infers their time traces in a way that is robust to as-yet unidentified neurons. To achieve real-time SEUDO (realSEUDO), we optimize the core estimator via both algorithmic improvements and an fast C-based implementation, and create a new cell finding loop to enable realSEUDO to also identify new cells. We demonstrate comparable performance to offline algorithms (e.g., CNMF), and improved performance over the current on-line approach (OnACID) at speeds of 120 Hz on average.