Started documenting actual steps

1 files changed, 40 insertions, 1 deletions

diff --git a/README.markdown b/README.markdown
index 3e301aa..c5dfc76 100644
--- a/README.markdown
+++ b/README.markdown
@@ -3,7 +3,7 @@ Automated Categorization of Drosophila Learning and Memory Behaviors using Video
 
 For more information about this project, goto:
 
-https://www.cs.drexel.edu/~david/Papers/Md_Reza_MS_Thesis.pdf
+https://www.cs.drexel.edu/~david/Papers/Md_Reza_MS_Thesis.pdf_
 
 This repository contains all of the source codes used for the Fly Tracking project.
 
@@ -35,3 +35,42 @@ The programs that will be built are located here:
 * ./fly-tools/standard-deviation
 * ./fly-tools/derive-background
 * ./fly-tools/filter-mask
+
+Dependencies
+------------
+
+Make sure you have these libraries and headers installed:
+
+* OpenCv
+* cvBlob
+* MagickWand
+* ImageMagick++  
+
+You will also need MPlayer to extract the PNGs.
+
+Usage
+-----
+
+Basically the fly tracking process takes several steps to complete. All of these
+steps can be automated with the process-video-beta script available in the
+scripts directory.
+
+=== Step 1 ===
+
+Since each video has several fly cells at one time, we need to crop each cell
+into it's own set. To do so, extract one frame of the video and then use gimp to
+determine the x, y, height and width of each cell (the select tool is very handy
+for this). You should write each cell into a file in this format: 
+
+  height:width:x:y
+
+You should save this in a file (make sure to name it properly. For the purpose
+of this explaination I am going to be working on video "Group1".
+
+Group1First10MinCropFile will look like this:
+
+  180:172:119:116
+  181:173:195:120
+  179:170:370:114
+
+