AlexTasks7 19 2018

1. Transform preprocessing notebook (notebooks/brain/preprocess/preprocess_cshl_data_v2_neurotrace.ipynb) into a scripts with argparse parameters.
2. Figure out the format of the files coming from UCSD and how they are translated to jp2000 (uncompressed)
3. Find a simple alternative to Yuncong's file-path-manager. (One idea: a script that asks you to enter directory paths and stores them in a configuration file and sets them into environmental variables). If file exists, just use it unless over-ride.
4. clean up old documentation. put historical links in a separate file.