Big Stitcher Parallel

These are functions and routines developed by Alon Oyler-Yaniv at the Wollman Lab at UCLA to streamline the processing of large, live, lightsheet datasets.

The pipeline is implemented in bash and is heavily dependent on ImageJ and Big Stitcher.

These functions work in tandem with the data acquisition software https://github.com/wollmanlab/Scope which automatically generates the parameters needed for processing.

To setup an analysis station follow these steps:

Start with a workstation running Ubuntu with a CUDA GPU

1. Install Nvidia drivers: $ ubuntu-drivers devices
2. check that the device is recognized and driver is suggested $ sudo ubuntu-drivers autoinstall
3. install nvidia-cuda-toolkit $ sudo apt install nvidia-cuda-toolkit
4. install pip
5. install conda
6. install ImageJ
7. pip install git
8. git clone https://github.com/alonyan/bigstitchparallel /Documents/Repos/bigstitchparallel
9. sudo apt-get install xvfb
10. symlink ImageJ: sudo ln -s .../ImageJ-linux64 /usr/local/bin/ImageJ