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

Blasse, Corinna; Saalfeld, Stephan; Etournay, Raphael; Sagner, Andreas; Eaton, Suzanne; Myers, Eugene W

doi:10.1093/bioinformatics/btx195

Item

ITEM ACTIONSEXPORT

Add to Basket

Local TagsRelease HistoryDetailsSummary

Released

Journal Article

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

MPS-Authors

There are no MPG-Authors in the publication available

External Resource

No external resources are shared

Fulltext (restricted access)

There are currently no full texts shared for your IP range.

Fulltext (public)

There are no public fulltexts stored in PuRe

Supplementary Material (public)

There is no public supplementary material available

Citation

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

Abstract

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.