de.mdc-berlin / cellsketch-create / 0.1.0

CellSketch: Create new project

These are exemplary masks which this solution imports into a joint BDV project.
This solution creates a new CellSketch project by importing the raw dataset as well as masks and labelings of cell components.
Citation Müller, D. Schmidt, C. S. Xu, S. Pang, J. V. D’Costa, S. Kretschmar, C. Münster, T. Kurth, F. Jug, M. Weigert, H. F. Hess, M. Solimena; 3D FIB-SEM reconstruction of microtubule–organelle interaction in whole primary mouse β cells. J Cell Biol 1 February 2021; 220 (2): e202010039.
10.1038/nmeth.3392Pietzsch, T., Saalfeld, S., Preibisch, S., & Tomancak, P. (2015). BigDataViewer: visualization and processing for large image data sets. Nature Methods, 12(6), 481–483.
Solution written by
Deborah Schmidt


The directory where a new CellSketch project will be created. (default value: PARAMETER_VALUE)
The name of the new project. (default value: PARAMETER_VALUE)
The raw dataset of the cell (3D). (default value: PARAMETER_VALUE)
Unit conversion factor from pixels to micrometers (default value: PARAMETER_VALUE)
Scale factor Z of input dataset (default value: 1)
Do not open the CellSketch Viewer after creating the project (default value: 0)

Usage instructions

Please follow this link for details on how to install and run this solution.