Aidan Daly, Ph.D.Guest Researcher, CCB, Flatiron Institute
Lisa M. Brown, Ph.D.Senior Data Scientist, Developmental Dynamics
Senior Project Lead, Data Visualization and Analysis, CCB, Flatiron Institute
1st presenter: Aidan Daly, PhD, Flatiron Research Fellow, Systems Biology
Topic: Bridging the gap between single-cell and spatially resolved -omics
Abstract: The development of spatially resolved -omics technologies allow us to probe mechanisms of tissue function and dysfunction that may be lost when studying dissociated tissue. Current technologies, however, suffer either from limited coverage (in situ hybridization methods) or limited resolution (spatial barcoding methods) when compared to bulk or single-cell approaches. In my talk, I will review approaches for integrating data from spatial and single-cell technologies, with a specific focus on deconvolution of spatial transcriptomics data into contributions attributable to distinct cells.
2nd presenter: Lisa Brown, PhD, Senior Data Scientist, Developmental Dynamics
Topic: 3D Segmentation and Tracking of Nuclei in Mouse Embryogenesis
Abstract: Unlike in many simpler model organisms, cell fate decisions in mammalian embryogenesis do not follow a precise pattern. To uncover the underlying mechanisms, we are working on automating 3D segmentation and tracking of nuclei in pre-implantation mouse embryos imaged with light-sheet microscopy. We have developed techniques useful for analyzing transcription dynamics up to the 32-cell stage. However, as the embryo continues to develop, the task becomes increasingly complicated, for the human as well as the computer. To assist human annotation, we’ve designed tools to integrate our initial results into our annotation interfaces. To improve our ability to segment as the cells divide and become tightly packed, we are in the process of training both 3D Mask RCNN [He 2017, Jaeger 2018] and 3D Stardist [Weigert 2020] models and will discuss our plans to leverage these complementary approaches.