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Whole-slide histology analysis pipeline scripts

Niko Kladt's picture
Workflow Author: 

Bastiaan G. L. Nelissen mail, Joost A. van Herwaarden, Frans L. Moll, Paul J. van Diest, Gerard Pasterkamp

Dependencies: 
Dimension: 
2D
Comment / Instructions: 

The publication describes a set of command-line tools to assist with the automated histology analysis of whole-slide images. This includes tools to organize the data, perform tiling and subsequent batch processing of the generated tiles in a cell profiler pipeline. All the tools are designed to run on a single PC or on a HPC system.

The scripts in the toolkit are on github under MIT licence.

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