AUTHOR=Mitani Akinori , Komiyama Takaki TITLE=Real-Time Processing of Two-Photon Calcium Imaging Data Including Lateral Motion Artifact Correction JOURNAL=Frontiers in Neuroinformatics VOLUME=12 YEAR=2018 URL=https://www.frontiersin.org/journals/neuroinformatics/articles/10.3389/fninf.2018.00098 DOI=10.3389/fninf.2018.00098 ISSN=1662-5196 ABSTRACT=

Two-photon calcium imaging has been extensively used to record neural activity in the brain. It has been long used solely with post-hoc analysis, but the recent efforts began to include closed-loop experiments. Closed-loop experiments pose new challenges because they require fast, real-time image processing without iterative parameter tuning. When imaging awake animals, one of the crucial steps of post hoc image analysis is correction of lateral motion artifacts. In most of the closed-loop experiments, this step has not been implemented and ignored due to technical difficulties. We recently reported the first experiments with real-time processing of calcium imaging that included lateral motion correction. Here, we report the details of the implementation of fast motion correction and present performance analysis across several algorithms with different parameters. Additionally, we introduce a novel method to estimate baseline calcium signal using kernel density estimate, which reduces the number of parameters to be tuned. Combined, we propose a novel software pipeline of real-time image processing suited for closed-loop experiments. The pipeline is also useful for rapid post hoc image processing.