de.mdc-berlin / cellsketch-mesh-export / 0.1.0

CellSketch: Export masks and labelmaps as meshes

Screenshot of a raw image next to the mesh generated from it and displayed using vtkplotlib.
VTK based mesh generation from pixel data, exports all masks and labelmaps from CellSketch project as meshes.
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.