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Image Analysis Upgrade for 3D Microscope Data Including Novel Multiplexed Batch Analysis Capability

Department of Physiology and Biophysics








This proposal requests a major software upgrade for the Keck Microscopy Center’s advanced 3D image analysis program, IMARIS, as well as the necessary hardware to fully support that upgrade. This upgrade will bring the Keck Center’s basic IMARIS license, with ~1/3 of available IMARIS functions, to a full version of the software with every available IMARIS function. Importantly, several of these image analysis functions are not currently available to UW student researchers in any UW core facility. IMARIS software is used to analyze the 3D microscopy data that UW student researchers produce with advanced microscopes either in the Keck Center, in another UW core facility, or in their own labs. A highly impactful and currently unavailable IMARIS function that would be included in this upgrade is the Batch module for processing multiple files simultaneously. This Batch module and the powerful computer hardware to support it could be used in conjunction with any of the other IMARIS modules, either currently available or newly available following this upgrade, to dramatically improve UW students’ image analysis capability and efficiency. No other core facility at the UW has a full version of IMARIS or is able to do Batch processing in IMARIS. Several additional IMARIS functions available in the full version of IMARIS are also not currently available to UW students. The Keck Center has provided microscopy training and services to hundreds UW students since its creation in 1990. In 2019, the Keck Center received STF funding for a confocal microscope software and hardware upgrade that provided a new Super-resolution confocal microscope capability to UW students, and it has already been instrumental in numerous UW student research projects. In 2020, despite a lockdown and restrictions due to COVID-19, 46 trained graduate students and 13 trained undergraduate students from over 40 labs in over 20 departments across the UW utilized the Keck Center for their research. The Keck Center is accessible to all UW students and its microscopy services are essential for UW student research in labs that cannot afford the advanced microscopy and image analysis services that the Keck Center provides. Numerous UW student researchers who use the Keck Center have specifically requested the IMARIS image analysis tools that would be provided by this proposed upgrade.

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