Update README.md

README.md

-# EmbedTrack - Global Linking
+# Global Cell Linking
 
-Project to provide Global linking of cell detection, based on the EmbedTrack method.
+Project to provide Global linking of cell detections.
+It is currently connected with an EmbedTrack segmentation routine.
 
 
 ***
 
+## Prerequisities
+
+- conda ![link](https://conda.io/projects/conda/en/latest/user-guide/install/index.html)
+- Gurobi Optimizer ![link](https://www.gurobi.com/downloads/gurobi-software/)
+
 ## Instalation
 
-First, clone the repository and update all its submodules. These are EmbedTrack an LibCT
+
+Clone the repository and update all its submodules. These are EmbedTrack an LibCT.
 
 
 ``` bash
@@ -17,7 +24,15 @@ git submodule update --init --recursive
 
 ```
 
-Load dataset CTC `BF-C2DL-HSC` to directory `DATA`. 
+Then, create the conda evironment.
+
+```bash
+conda env create -f GlobalTracking.env
+conda activate GlobalTracking
+```
+
+
+Load dataset CTC `BF-C2DL-HSC` to directory `DATA`.  
 The final structure should should be following:
 
 ```
@@ -25,22 +40,20 @@ The final structure should should be following:
 --DATA
     -- 'SUBSET'                             # Subset is 'train' or 'challenge'
         -- 'DATASET_NAME'                   # Name of dataset e.g. 'BF-C2DL-HSC
-            -- config.yml                   # Deepwater configuration file
             -- 01                           # YY - name of sequence, a two digit number, e.g. '01', '02'
-                -- t000.tif
-                -- t001.tif
+                -- t0000.tif
+                -- t0001.tif
                 ...
-                -- tXXX.tif
             -- 01_GT                        # GT, 'train' subset only
                 -- SEG                      # segmentation reference
-                    -- man_seg000.tif
-                       ...
-                    -- man_segXXX.tif
+                    -- man_seg0000.tif
+                    -- man_seg0001.tif
+                    ...
                 -- TRA                      # tracking reference
-                    -- man_track000.tif
-                      ...
-                    -- man_trackXXX.tif
                     -- man_track.txt
+                    -- man_track0000.tif
+                    -- man_track0001.tif
+                      ...
 ```
 
 Open the notebook