Principles of cell and tissue organization
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A versatile pipeline for the multi-scale digital reconstruction and quantitative analysis of 3D tissue architecture

In this study published in eLife we developed a pipeline for the reconstruction and quantitative analysis of tissue architecture in 3D. Using a combination of newly developed and stablished image analysis algorithms, our pipeline allows for a flexible workflow to reconstruct the different structures forming the tissue with superior accuracy. As proof of principle, we applied it to the analysis of mouse liver tissue. In describing its 3D structure in detail, we revealed an unexpected spatial distribution of cells having distinct volume and DNA content within the tissue. Moreover, we performed a digital reconstruction of structurally distinct tissues such as lung and kidney, demonstrating its general applicability. This pipeline can be used for several applications from basic (understanding of how cells form tissues) to clinical research (diagnosis of diseases by 3D digital histology). The pipeline was implemented as part of the stand-alone freely available software MotionTracking (http://motiontracking.mpi-cbg.de). 

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