Installation

The main modules are all written in C++ and compiled to executable binaries. The overall pipeline wrapper is a python script. If you are running this pipeline at Janelia, the only installation necessary is to ensure that these binaries and pythons scripts are on your path. If you would like to rebuild the pipeline elsewhere, please see additional information below.

Dependencies

• boost-program-options >= 1.73.0
• boost-filesystem >= 1.73.0
• ITK >= 5.1.0
• Python >= 3.8.2
• CMake

The pipeline assumes that all LLSM settings files have been generated by v4.04505.Development of the LLSM control software. Settings files generated by different versions of the LLSM control software are not likely to be parsed correctly by our parsing routine.

Module Building

The LLSM pipeline was purpose built to run on the Janelia cluster. For example, the pipeline assumes that it can directly submit jobs to an LSF cluster. We recommend using VCPKG to install the necessary dependencies.

vcpkg install itk boost-program-options boost-filesystem

Once the dependencies are installed, use CMake to build the binaries.