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Segmenting, analyzing and visualizing volumetric Electron Microscopy datasets
io.github.betaseg
/
cellsketch-mesh-export
/ 0.1.0
CellSketch: Export masks and labelmaps as meshes
VTK based mesh generation from pixel data, exports all masks and labelmaps from CellSketch project as meshes.
Citation
Schroeder, W.; Martin, K.; Lorensen, B. (2006). The Visualization Toolkit (4th ed.), Kitware, ISBN 978-1-930934-19-1
https://vtk.org/
10.5281/ZENODO.3585752
Pape, C. (2019). constantinpape/z5
Solution written by
Deborah Schmidt
Arguments
--project
The CellSketch project (ends with .n5) (default value: PARAMETER_VALUE)
--include
List of names of elements which should be loaded, comma separated (default value: PARAMETER_VALUE)
--exclude
List of names of elements which should not be loaded, comma separated (default value: PARAMETER_VALUE)
--headless
Do not display mesh after processing it. Set this to true if you run into memory issues. (default value: 0)
Usage instructions
Please follow
this link
for details on how to install and run this solution.