Cortex-wide In-vivo Two-photon Calcium Imaging Analysis of Mice During Skilled Reaching

Document Type


Publication Date

Summer 2023



JAX Location

In: Student Reports, Summer 2023, The Jackson Laboratory


Neural plasticity post-stroke induces circuit-level changes in neuronal connectivity in surviving cortical regions. An understanding of cortical interactions across regions in the normal brain allows for determining maladaptive mechanisms that arise after a stroke. Mesoscopic two-photon calcium imaging data, acquired from multiple brain regions during skilled reaching, provides a deeper comprehension of brain-circuit connectivity patterns in the healthy brain and could help further understand the rules guiding reconnection of damaged networks during recovery of skilled limb function post-stroke. We implemented a cortex-wide analysis from recordings of PT projection class neurons in five motor cortical regions for detection and extraction of neural activity traces. Here, using, published methodologies, we develop a pipeline for the analysis of high-dimensional neural activity data and measures of network connectivity obtained in mice performing a skilled reaching task with the overarching goal of applying this to the stroke brain. We adapted and benchmarked two python-based toolboxes for processing of two-photon calcium imaging recordings and applied this pipeline to a large-sized datasets. Additionally, implementing this pipeline to different projection classes will reveal circuit-based differences during skill reaching. Automatization of these algorithms to require minimal user input will facilitate future studies contrasting circuit activity in the healthy brain compared to that of the stroke brain.

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