Update README.md

README.md

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 Project to provide Global linking of cell detection, based on the EmbedTrack method.
 
 
-
-
-## Steps to Complete the Repository
-
-- [ ] [include the EmbedTrack library]
-- [ ] [add a call EmbedTrack inference procedure from outside the library]
-- [ ] [add a call of the tracking procedure]
-- [ ] [add visualization in a blender]
-- [ ] [complete instalation and requirements.txt]
-- [ ] [document how the package is used]
-- [ ] [add CTC evaluation]
-
 ***
 
+## Instalation
+
+First, clone the repository and update all its submodules. These are EmbedTrack an LibCT
+
+
+``` bash
+git clone https://gitlab.fi.muni.cz/xlux/global-linking.git
+git submodule update --init --recursive
+
+```
+
+Load dataset CTC `BF-C2DL-HSC` to directory `DATA`. 
+The final structure should should be following:
+
+```
+# Structure of training data directory
+--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
+                ...
+                -- tXXX.tif
+            -- 01_GT                        # GT, 'train' subset only
+                -- SEG                      # segmentation reference
+                    -- man_seg000.tif
+                       ...
+                    -- man_segXXX.tif
+                -- TRA                      # tracking reference
+                    -- man_track000.tif
+                      ...
+                    -- man_trackXXX.tif
+                    -- man_track.txt
+```
+
+Open the notebook
+
+``` bash
+./run_notebook.sh
+```
 
 
 ## Description