Semi-Automatic Generation of Tight Binary Masks and Non-Convex Isosurfaces for Quantitative Analysis of 3D Biological Samples

• URL: http://arxiv.org/abs/2001.11469v1
• Date: Thu, 30 Jan 2020 17:36:42 GMT
• Title: Semi-Automatic Generation of Tight Binary Masks and Non-Convex Isosurfaces for Quantitative Analysis of 3D Biological Samples
• Authors: Sourabh Bhide, Ralf Mikut, Maria Leptin, Johannes Stegmaier
• Abstract summary: Current microscopy allows us (3D+t) of complete organisms (3D+t) to offer insights into their development on the cellular level. Even though imaging speed and quality is steadily improving, fully- segmentation analysis methods are not accurate enough. This is true while imaging (100um - 1mm) and deep inside the specimen. We developed a system for analyzing quantitatively 3D+t light-sheet microscopy images of embryos.
• Score: 0.2711107673793059
• License: http://arxiv.org/licenses/nonexclusive-distrib/1.0/
• Abstract: Current in vivo microscopy allows us detailed spatiotemporal imaging (3D+t) of complete organisms and offers insights into their development on the cellular level. Even though the imaging speed and quality is steadily improving, fully-automated segmentation and analysis methods are often not accurate enough. This is particularly true while imaging large samples (100um - 1mm) and deep inside the specimen. Drosophila embryogenesis, widely used as a developmental paradigm, presents an example for such a challenge, especially where cell outlines need to imaged - a general challenge in other systems as well. To deal with the current bottleneck in analyzing quantitatively the 3D+t light-sheet microscopy images of Drosophila embryos, we developed a collection of semi-automatic open-source tools. The presented methods include a semi-automatic masking procedure, automatic projection of non-convex 3D isosurfaces to 2D representations as well as cell segmentation and tracking.

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