CellSketch

Authors: Deborah Schmidt, Martin Weigert, Andreas Müller, Lucas Rieckert

Keywords: visualization

CellSketch is used to collect masks and labels belonging to the same 3D scene into one project. The routines are primarily targeting but not limited to single cell datasets. All imported datasets are stored in the N5 format as blocks. They can be displayed with BigDataViewer. All labels imported as labelmaps can be spatially analyzed in relation to other labelmaps and masks. Results are stored as tables. A routine for generating plots based on the analysis is provided as well. Finally, masks and labelmaps can be exported as meshes, displayed with VTK and rendered using Blender.


Publications

Organelle-specific segmentation, spatial analysis, and visualization of volume electron microscopy datasets

Müller A, Schmidt D, Rieckert L, Solimena M, Weigert M - arXiv - 2023


3D FIB-SEM reconstruction of microtubule–organelle interaction in whole primary mouse β cells

Müller A, Schmidt D, Xu C, Pang S, D’Costa J, Kretschmar S, Münster C, Kurth T, Jug F, Weigert M, Hess H, Solimena M - Journal of Cell Biology - 2020


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