add readme

README.md

+##Setup
+### 1) create folder structure
+- create local directory LOCAL_DIR
+- clone code to LOCAL_DIR
+- add folders data and results in LOCAL_DIR
+so the final structure is  
+--LOCAL_DIR  
+    |  
+    -- data (contains the ground truth data sets)  
+    |       
+    -- code   
+    |     
+    -- results (synthetically degraded segmentation masks stored will be stored here)
+### 2) create environment
+- install packages from requirements
+- install gurobi 9.1.1 (see help_gurobi.txt)
+
+## run tracking
+
+## Reproduce data sets
+### 1) download data sets
+- go to http://celltrackingchallenge.net
+and download : Fluo-N2DH-SIM+ and FLuo-N3DH-SIM+ and unpack and save in data directory
+
+### 2) run code
+- run create_synth_segm_data.py to create synthetically 
+

help_gurobi.txt

+In the tracking step a solver (Gurobi) is used to solve integer linear programs
+For academic purposes, Gurobi provides an academic license free of charge.
+
+To run the tracking, Gurobi needs to be installed:
+1) register at https://www.gurobi.com
+if academia: select academic license
+
+2)download gurobi optimizer version 9.1.1 from https://www.gurobi.com/downloads/gurobi-software/
+
+3) move download to a local directory (LOCAL_DIR)
+mv /../Downloads/gurobi9.1.1_linux64.tar.gz /LOCAL_DIR
+
+4) change to local dir and unzip
+tar xvfz gurobi9.1.1_linux64.tar.gz
+
+5) add gurobi to path
+export=$PATH:/LOCAL_DIR/gurobi911/linux/bin
+
+6) get gurobi license key https://www.gurobi.com/downloads/end-user-license-agreement-academic/
+
+7) copy license key to comand line
+grbgetkey xxxx-xxxx-xxx
+hit enter (select provided default directory to store license file)
+
+8) run tracking