4D Cell Biology: Adaptive optics lattice light sheet imaging and AI powered big data processing of live stem cell derived organoids.
New methods in stem cell 3D organoid tissue culture, advanced imaging, and big data image analytics now allow tissue scale 4D cell biology but currently available analytical pipelines are inadequate for handing and analyzing the resulting gigabytes and terabytes of high content imaging data. We expressed fluorescent protein fusions of clathrin and dynamin2 at endogenous levels in genome edited human embryonic stem cells, which were differentiated into intestinal epithelial organoids. Lattice light sheet imaging with adaptive optics (AO LLSM) allowed us to image large volumes of these organoids (70 x 60 x 40 mm xyz) at 5.7 s/frame. We developed an open source data analysis package termed pyLattice to process the resulting large ~60 Gb) movie data sets and to track clathrin mediated endocytosis (CME) events. We then expressed fluorescent protein fusions of actin and tubulin in genome edited induced human pluripotent stem cells, which were differentiated into human cortical organoids. Using the AO LLSM mode on the new MOSAIC (Multimodal Optical Scope with Adaptive Imaging Correction) allowed us to image neuronal migration deep in the organoid. We augmented pyLattice with a deep learning module and used it to process the brain organoid data.
Journal of biomolecular techniques JBT