Decomposition–Estimation–Reconstruction: An Automatic and Accurate Neuron Extraction Paradigm

The extraction of spatiotemporal neuron activity from calcium imaging videos plays a crucial role in unraveling the coding properties of neurons. While existing neuron extraction approaches have shown promising results, disturbing and scattering background and unused depth still impede their performance. To address these limitations, we develop an automatic and accurate neuron extraction paradigm, dubbed as decomposition-estimation-reconstruction (DER), consisting of D-procedure, E-procedure, and R-procedure. Specifically, the D-procedure first decomposes the raw data into a low-rank background and a sparse neuron signal, and regularizes L₀ -norm priors of intensity and gradient of the neuron signal to suppress blurring and artifact effects. Then, the E-procedure estimates the depth-dependent transmission of the neuron signal based on its bright and dark channel priors. The R-procedure finally integrates the depth estimation of the neuron signal as a content-importance weight into a constrained non-negative matrix decomposition framework, which facilitates accurate neuron locations to boost the quality of extracted neurons. These three procedures are coupled in a cascade manner, where the former copes with calcium imaging data to facilitate the subsequent one. Comprehensive experiments on neuron extraction from calcium imaging videos demonstrate the superiority of our DER paradigm in both qualitative results and quantitative assessments over state-of-the-art methods.