Data S1: Technical drawings of adaptive light-sheet microscope, computational tools for image analysis, and dynamic cellular atlas of mouse development

Published: 4 October 2018| Version 1 | DOI: 10.17632/fky6dkhmb3.1
Contributor:
Philipp Keller

Description

This data file contains the following resources: 1) A complete blueprint of the adaptive multi-view light-sheet microscope for mouse imaging, including technical drawings of the microscope’s 77 types of custom mechanical components, assembly illustrations for the microscope’s 28 types of multi-part assemblies, and parts list of all custom and commercial mechanical microscope components. 2) Computational tools for image analysis, including software modules for KLB image compression, block-matching multi-view/time-lapse image registration, multi-view image deconvolution, division detection with a convolutional neural network, TGMM 2.0 cell tracking with a machine-learning module, statistical vector flow (SVF) analysis, interactive 4D visualization of SVF databases, spatiotemporal registration of multiple embryos with TARDIS, and average embryo database query using external label masks. 3) Dynamic cellular atlas of mouse development, including databases of cell tracks with tissue annotations for four embryos (TARDIS embryos A-D), an interactive visualization of annotated cell tracks for TARDIS embryo A, database of cell divisions for TARDIS embryo A, landmark annotations in the average embryo, TARDIS statistical fate map (statistical integration of four embryos), the average embryo (statistical integration of four embryos), database of tissue morphodynamics for TARDIS embryo A, and the TARDIS database of tissue morphodynamics (statistical integration of four embryos).

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Institutions

Howard Hughes Medical Institute Janelia Farm Research Campus

Categories

Mouse, Organogenesis, Biomedical Imaging, Mapping, Atlas, Light Microscopy, Embryonic Development, Neural Networks, Gastrulation, Image Analysis, Object Tracking (Computer Vision)

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