SomaSeg: a robust neuron identification framework for two-photon imaging video.

Objective.Accurate neuron identification is fundamental to the analysis of neuronal population dynamics and signal extraction in fluorescence videos. However, several factors such as severe imaging noise, out-of-focus neuropil contamination, and adjacent neuron overlap would impair the performance of neuron identification algorithms and lead to errors in neuron shape and calcium activity extraction, or ultimately compromise the reliability of analysis conclusions.Approach.To address these challenges, we developed a novel cascade framework named SomaSeg. This framework integrates Duffing denoising and neuropil contamination defogging for video enhancement, and an overlapping instance segmentation network for stacked neurons differentiating.Main results.Compared with the state-of-the-art neuron identification methods, both simulation and actual experimental results demonstrate that SomaSeg framework is robust to noise, insensitive to out-of-focus contamination and effective in dealing with overlapping neurons in actual complex imaging scenarios.Significance.The SomaSeg framework provides a widely applicable solution for two-photon video processing, which enhances the reliability of neuron identification and exhibits value in distinguishing visually confusing neurons.