SourceExtraction

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

Name		Name	Last commit message	Last commit date
Latest commit History 42 Commits
.ipynb_checkpoints		.ipynb_checkpoints
.gitattributes		.gitattributes
.gitignore		.gitignore
AuxilaryFunctions.py		AuxilaryFunctions.py
BlockGroupLasso.py		BlockGroupLasso.py
BlockLocalNMF.py		BlockLocalNMF.py
BlockLocalNMF_AuxilaryFunctions.py		BlockLocalNMF_AuxilaryFunctions.py
CNMF4Dendrites.py		CNMF4Dendrites.py
CompareGroundTruth.py		CompareGroundTruth.py
Create_Colors.py		Create_Colors.py
Demo.cprof		Demo.cprof
Demo.py		Demo.py
PlotComparison2GroundTruth.py		PlotComparison2GroundTruth.py
PlotCorrelations.py		PlotCorrelations.py
PlotResults.py		PlotResults.py
README.md		README.md
Simple_demo.py		Simple_demo.py
colormaps.py		colormaps.py
data_small		data_small
dsp_dend.tif		dsp_dend.tif

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