de.mdc-berlin / cellsketch-analyze / 0.1.0

CellSketch: Run spatial analysis

This solution performs spatial analysis for all organelles in a CellSketch project.
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 CellSketch project to be opened (.n5). (default value: PARAMETER_VALUE)
Max distance between two connected organelles in μm. (default value: PARAMETER_VALUE)
Do not recalculate existing distance transform maps. (default value: 0)

Usage instructions

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