System Requirements

To run ExSequence the following OS and software is required:

• Linux: A Linux OS is required; ExSequence assumes Linux paths and tools are available. Testing has been done on CentOS 7.
• Bash: The main pipeline script (runPipeline.sh) which launches the other MATLAB scripts uses bash.
• MATLAB: Most of the functionality of ExSequence is contained in MATLAB scripts and is required
• (optional) CUDA: Allows for using NVIDIA GPUs to accelerate some stages of ExSequence pipeline. This is not required to run the pipeline however if available can be used to significantly reduce time taken to run.
• (optional) Python: Is used for setting parameters in a GUI or an interactive command line interface. These same parameters can be set by pipeline script options or by setting them in loadParameters.m file. It is also necessary for using a performance profile option of the pipeline. Python major versions 2 and 3 are supported.
• (optional) Jupyter, numpy, pandas, matplotlib: These are additional Pyhton tools and libraries necessary for displaying the results of the performance profile option.

RAM requirements depend on the size of the input dataset as well as the degree of parallelization used. Using multiple process reduces the time taken by the pipeline requires having sufficient memory.

Disk usage also depends on the input data size. The colour correction and registration stages create full copies of the data and normalization stage creates one file per round. These stages also optionally create down sampled versions further increasing the size. The output produced increases disk usage to roughly 3-4 times the original size after running the pipeline.