6 research outputs found
Recovering the Imperfect: Cell Segmentation in the Presence of Dynamically Localized Proteins
Deploying off-the-shelf segmentation networks on biomedical data has become
common practice, yet if structures of interest in an image sequence are visible
only temporarily, existing frame-by-frame methods fail. In this paper, we
provide a solution to segmentation of imperfect data through time based on
temporal propagation and uncertainty estimation. We integrate uncertainty
estimation into Mask R-CNN network and propagate motion-corrected segmentation
masks from frames with low uncertainty to those frames with high uncertainty to
handle temporary loss of signal for segmentation. We demonstrate the value of
this approach over frame-by-frame segmentation and regular temporal propagation
on data from human embryonic kidney (HEK293T) cells transiently transfected
with a fluorescent protein that moves in and out of the nucleus over time. The
method presented here will empower microscopic experiments aimed at
understanding molecular and cellular function.Comment: Accepted at MICCAI Workshop on Medical Image Learning with Less
Labels and Imperfect Data, 202
Quantifying the progression of non-alcoholic fatty liver disease in human biomimetic liver microphysiology systems with fluorescent protein biosensors
Construction of a Multiwell Light-Induction Platform for Traceless Control of Gene Expression in Mammalian Cells
Mammalian cells can be engineered to incorporate light-responsive elements that reliably sense stimulation by light and activate endogenous pathways, such as the cAMP or Ca2+ pathway, to control gene expression. Light-inducible gene expression systems offer high spatiotemporal resolution, and are also traceless, reversible, tunable, and inexpensive. Melanopsin, a well-known representative of the animal opsins, is a G-protein-coupled receptor that triggers a Gαq-dependent signaling cascade upon activation with blue light (≈470 nm). Here, we describe how to rewire melanopsin activation by blue light to transgene expression in mammalian cells, with detailed instructions for constructing a 96-LED array platform with multiple tunable parameters for illumination of the engineered cells in multiwell plates.ISSN:1064-3745ISSN:1940-602