Publications [#356415] of Sina Farsiu

Papers Published

1. Bao, Y; Soltanian-Zadeh, S; Farsiu, S; Gong, Y, Segmentation of Neurons from Fluorescence Calcium Recordings Beyond Real-time., Nature machine intelligence, vol. 3 no. 7 (July, 2021), pp. 590-600 [doi]
   (last updated on 2024/12/31)

   Abstract:
   Fluorescent genetically encoded calcium indicators and two-photon microscopy help understand brain function by generating large-scale in vivo recordings in multiple animal models. Automatic, fast, and accurate active neuron segmentation is critical when processing these videos. In this work, we developed and characterized a novel method, Shallow U-Net Neuron Segmentation (SUNS), to quickly and accurately segment active neurons from two-photon fluorescence imaging videos. We used temporal filtering and whitening schemes to extract temporal features associated with active neurons, and used a compact shallow U-Net to extract spatial features of neurons. Our method was both more accurate and an order of magnitude faster than state-of-the-art techniques when processing multiple datasets acquired by independent experimental groups; the difference in accuracy was enlarged when processing datasets containing few manually marked ground truths. We also developed an online version, potentially enabling real-time feedback neuroscience experiments.