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.
Tags
templatenapari
Citation
https://doi.org/10.1083/jcb.202010039A. 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

Arguments

--parent
The directory where a new CellSketch project will be created. (default value: PARAMETER_VALUE)
--name
The name of the new project. (default value: PARAMETER_VALUE)
--input
The raw dataset of the cell (3D). (default value: PARAMETER_VALUE)
--pixel_to_um
Unit conversion factor from pixels to micrometers (default value: PARAMETER_VALUE)
--scale_z
Scale factor Z of input dataset (default value: 1)
--headless
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.