Update readme.md

readme.md

@@ -2,5 +2,49 @@ This is a repository for the manuscript and accompanying code currently under de
 
 Once the manuscript is released, all code will be licensed open source (license TBD, likely GPL or BSD).
 
-questions? contact andrew.r.cohen 'at' drexel.edu
+Questions? contact andrew.r.cohen 'at' drexel.edu 
  
+ # INSTALLATION 
+
+## Prerequisites 
+
+1. Clone the required repositories:
+
+```
+git clone https://git-bioimage.coe.drexel.edu/opensource/rsf.git
+```
+and
+```
+git clone https://git-bioimage.coe.drexel.edu/opensource/ncd.git
+```
+and
+HIP (how to install, use git? or install via HIP website?)
+
+```
+git clone https://git-bioimage.coe.drexel.edu/opensource/hydra-image-processor.git
+```
+
+2. 
+
+NODE? Right now required bececause of lever and lever utils dependencies.
+
+## MATLAB Configuration  
+MATLAB version number minimum requirement?
+
+Create a sample startup.m file in the rsf\src\MATLAB folder?
+
+https://www.mathworks.com/help/matlab/ref/startup.html
+
+USER is the username of the user running the RSF code. The path should reflect where the git install was located, in this example case in the USER folder.
+
+```
+addpath(genpath,('C:\Users\USER\hydra-image-processor\src\MATLAB'));
+addpath(genpath('C:\Users\USER\ncd\src\MATLAB'));
+addpath(genpath('C:\Users\USER\rsf\SRC\MATLAB'));
+```
+
+## Pipeline
+
+1. Import images, sameple import code
+
+2. Run?
\ No newline at end of file