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Igor Pisarev edited this page Jul 1, 2020
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Pipeline steps and input parameters are explained in the README.
Full list of parameters (including optional and experimental ones):
- Flatfield correction parameters
- Stitching parameters
- N5 export parameters
- N5 export to slice TIFF conversion parameters
The pipeline can be run locally or on an HPC cluster that has Apache Spark installed. Please see how to use the startup scripts for local machine runs and Janelia cluster in the main README.
For running on popular cloud platforms, please see these pages:
The main branch uses translation-only registration of tiles. Support for affine models is experimental and is available in this branch: https://github.com/saalfeldlab/stitching-spark/tree/affine-stitching-with-uncertainty
The experimental affine-based registration algorithm is described in this wiki page: Affine stitching algorithm