Beckman Foundation Awards Center Grant for Advanced Lightsheet Microscopy and Data Science

Abstract:

There are two main goals for our Beckman Foundation Light Sheet Microscopy Center program.  The overall research goal is to build a robust data handling pipeline for the big data inherent in light sheet microscopy.  We aim to achieve this goal in concert with our second goal of proactively fostering the careers of junior faculty, postdoctoral trainees, and students.  These goals will be accomplished by empowering and leveraging existing biomedical research projects to engage with data science collaborators.  We are designing this pipeline to facilitate data handling through the steps of fusion, reduction, and analysis.  For data fusion, we will assemble and reconstruct 3D datasets as needed for tomographic reconstruction, stitch together tiled 3D datasets, combine spectral and spatial data, or perform any combination of these actions.  Data reduction is often critical given the large size of the datasets.  We expect that it will be enabling for users to be able to reduce data to its essential parts for examination, although we will always maintain the complete raw data linked to the reduced dataset.  This reduction could focus around spatial sub-regions, or identification of specific objects (i.e., vesicles in a cell or cells in a tissue) followed by analyzing only the identified objects.  Analysis will encompass anything from classifying groups of objects in the 3D dataset (i.e., by fluorescence signal or morphology), segmenting those individual objects within specific groups, or conducting analyses on classified/segmented objects over time (i.e. number, volume, contact sites, distance measurements, object tracking).  To guide the analysis pathway development, we have chosen three key projects representing broad research areas that are already using light sheet microscopy and span spatial scales from sub-cellular to humans.  These three labs, headed by two Assistant Professors and one Associate Professor, each have funded projects that are limited by imaging technology.  These labs were chosen due to their active participation in developing synergy with the data science collaboration.  We have also identified another six labs (two led Assistant Professors) that will participate with closely-aligned research projects.  All 9 of these labs have data handling/analysis bottlenecks that are slowing research progress, and all will benefit from the faster data acquisition rates with the proposed lattice light sheet microscope – either to image dynamics at higher rates, or to image larger fields faster.