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Journal Article

PreMosa: extracting 2D surfaces from 3D microscopy mosaics.

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Blasse, C., Saalfeld, S., Etournay, R., Sagner, A., Eaton, S., & Myers, E. W. (2017). PreMosa: extracting 2D surfaces from 3D microscopy mosaics. Bioinformatics (Oxford, England), 33(16), 2563-2569. doi:10.1093/bioinformatics/btx195.

Cite as: https://hdl.handle.net/21.11116/0000-0002-8C9C-1
A significant focus of biological research is to understand the development, organization and function of tissues. A particularly productive area of study is on single layer epithelial tissues in which the adherence junctions of cells form a 2D manifold that is fluorescently labeled. Given the size of the tissue, a microscope must collect a mosaic of overlapping 3D stacks encompassing the stained surface. Downstream interpretation is greatly simplified by preprocessing such a dataset as follows: (i) extracting and mapping the stained manifold in each stack into a single 2D projection plane, (ii) correcting uneven illumination artifacts, (iii) stitching the mosaic planes into a single, large 2D image and (iv) adjusting the contrast.