Rapid Evaluation of Neuronal Activity in the Intact Whole Brain at Single Cell Resolution

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Project Summary Here we seek to develop a “Neuronal Activity Quantitative Diagnostic” platform and reagent kits to disseminate accessible products for measuring recent neural activity across the entire mouse brain to the neuroscience community. Previously we have shown that the activity-dependent immediate-early gene protein products Npas4 and cFos can be clearly detected, imaged, and quantified using developmental versions of our platform tools. Immediate early genes are genes that are activated transiently and rapidly in response to a wide variety of cellular stimuli. The three overlapping aims to be investigated in this Phase II project are: 1) Demonstration of the fidelity of our assay for our customers. To demonstrate the robustness and accuracy of our neuronal activity assay with another well-known assay for activity, we will perform two photon calcium fluorescence imaging in the primary visual cortex of mice presented with repeated visual stimuli. We will clear and stain the brains for cFos and Npas4 and demonstrate the fidelity of these markers for detecting recently active neurons. 2) Develop and beta test robust versions of our software tools useable by researchers with no specialized coding or statistics knowledge. We will develop Stitchy and BrainSnap into robust, user-friendly software products that remove the current analysis bottleneck for neuroscientists interested in whole-brain imaging. Stitchy will be an improved browser-based version of our internal software that simplifies and speeds the process of stitching together light sheet microscope images. BrainSnap software will integrate our high-performance 3TK- Quant framework for machine learning-enabled quantification and our statistical framework for whole-brain anatomics, 3TK-Stats, in a browser-based interface. We have recruited end users who will test this software in a head-to-head comparison with our in-house testing. 3) Develop and test a brain clearing and staining kit for neuronal activity. To help researchers produce high quality cleared brains stained with neuronal activity markers, we will generate Neuronal Activity clearing and staining reagents kits for cFos and Npas4. These will be tested by collaborators in head-to-head comparisons with our in-house procedures on brains prepared in parallel. At the end of Phase II, Translucence will have a market-ready Neuronal Activity Quantitative Diagnostic platform including reagent kits, user-friendly software, and service options.