constantinpape / mc_luigi

Multicut workflow for processing large-scale connectomics data, using luigi for pipelining.

This repository is deprecated, have a look at cluster_tools instead.

McLuigi

Multicut workflow for large connectomics data. Using luigi for pipelining and caching processing steps. Most of the computations are done out-of-core using hdf5 as backend and implementations from nifty

Installation

You need a cplex or gurobi license to use the multicut pipeline.

conda (recommended)

To fulfill all dependencies, you also need to have the ilastik and conda-forge channel in your .condarc . Then install the package via

$ GUROBI_ROOT_DIR=/path/to/gurobi conda install -c cpape mc_luigi=0.1 

The current package only supports gurobi as solver backend, please make an issue if you need a version with cplex.

From source

You can also install the dependencies from source:

• Luigi: https://github.com/spotify/luigi (version 2.3)
• Vigra: https://github.com/ukoethe/vigra (master, needs to be build with hdf5 and python-bindings)
• Nifty: https://github.com/constantinpape/nifty/tree/stacked_rag , needs to be build with python-bindings, hdf5, fastfilters (https://github.com/svenpeter42/fastfilters) and Gurobi or CPLEX.

Missing Features

• Lifted Multicut
• Pipeline for isotropic data.

TODOs

• Get central scheduler running.
• Add docstrings
• change to PEP8 style