update README and remove old content

Updated README to clarify usage instructions and removed outdated section.

Author: trangle1302

README.md

@@ -101,13 +101,7 @@ python s4_concentric_rings_intensity.py
 OR
 Protein morphing on to shape based on [thin-plate splines](https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=24792) given landmarks: nucleus centroid, 32p in nucleus membrane, 32p cell membrane. Final shape for all proteins = shape of the average cell in that shapemode (bin).
 ```sh
-python s4_protein_image_warp.py
-```
-
-### s5 - Organelle distribution and relation with each other
-
-```sh
-python s5_organelle_heatmappy
+python s4_protein_image_warp.py # check other variations in the same folder
 ```
 
 The pilot was performed for a small subset of U2OS cell line (private images, manual segmentation and annotations): cells (1776 images) as well as HPA (public images, automatic segmentation): 297108 cells (23272 images). For historical reason, some files contained fixed paths, such as [shapemode_pipeline.py](shapemode_pipeline.py).