Code for extracting axons and dendrite from Calcium data
Installation: Requires Python 2.7 and 3.5. Download to folder. Download and install OASIS (together with its dependencies) from here: https://github.com/j-friedrich/OASIS and add as a subfolder. Additional dependencies: all the WinPython libraries, tifffile... and maybe more.
Main files:
Simple_Demo.py - Run this to see how basic code works (on small 3D data sample).
Demo.py - More advanced options and parameters for many datasets. Run to see how code works, in more detail.
BlockLocalNMF.py - main script for running a single NMF repetition. LocalNMF code contains description of all input parameters.
AuxilaryFunctions.py - General Auxilary Functions
BlockLocalNMFAuxilaryFunctions.py - Auxilary Functions for BlockLocalNMF
PlotResults.py - plotting functions