add images in documentation and readme

Author: Henley13

README.md

@@ -9,6 +9,18 @@
 
 **Sim-FISH** is a python package to **simulate smFISH images**. The package allows the user simulate and localize spots, cells and nuclei. The ultimate goal is to provide toy images to **experiment, train and evaluate smFISH statistical analysis**.
 
+User can simulate images of spots and clusters with different level of noise...
+
+| Spots | Clustered  spots |
+| ------------- | ------------- |
+| ![](images/plot_spot.png "Spots") | ![](images/plot_cluster_zoom.png "Clustered spots") |
+
+... or localization patterns within  subcellular regions.
+
+| Perinuclear pattern | Protrusion pattern |
+| ------------- | ------------- |
+| ![](images/perinuclear_1_300.png "Perinuclear pattern") | ![](images/protrusion_1_300.png "Perinuclear pattern") |
+
 ## Installation
 
 ### Dependencies

docs/source/image_simulation.rst

@@ -7,6 +7,19 @@ Image simulation
 
 Functions used to simulate spot images, in 2D and 3D.
 
++------------------+------------------+------------------+
+|      |pic1|      |      |pic2|      |      |pic3|      |
++------------------+------------------+------------------+
+
+.. |pic1| image:: ../../images/plot_spot.png
+   :width: 100%
+
+.. |pic2| image:: ../../images/plot_cluster_zoom.png
+   :width: 100%
+
+.. |pic3| image:: ../../images/plot_cluster.png
+   :width: 100%
+
 Simulation is performed in three steps:
 
 #. We simulate ground truth coordinates.

docs/source/index.rst

@@ -6,6 +6,19 @@
 Sim-FISH
 ********
 
++------------------+------------------+------------------+
+|      |pic1|      |      |pic2|      |      |pic3|      |
++------------------+------------------+------------------+
+
+.. |pic1| image:: ../../images/plot_spot.png
+   :width: 100%
+
+.. |pic2| image:: ../../images/plot_cluster_zoom.png
+   :width: 100%
+
+.. |pic3| image:: ../../images/perinuclear_1_300.png
+   :width: 100%
+
 Getting started
 ===============
 

docs/source/pattern_simulation.rst

@@ -7,6 +7,41 @@ Pattern simulation
 
 Functions used to simulate localization patterns.
 
++------------------+------------------+------------------+
+|    **Random**    |     **Foci**     | **Intranuclear** |
++------------------+------------------+------------------+
+|      |pic1|      |      |pic2|      |      |pic3|      |
++------------------+------------------+------------------+
+| **Nuclear_edge** |  **Perinuclear** |   **Cell_edge**  |
++------------------+------------------+------------------+
+|      |pic4|      |      |pic5|      |      |pic6|      |
++------------------+------------------+------------------+
+|  **Protrusion**  |                  |                  |
++------------------+------------------+------------------+
+|      |pic7|      |                  |                  |
++------------------+------------------+------------------+
+
+.. |pic1| image:: ../../images/random_1_300.png
+   :width: 100%
+
+.. |pic2| image:: ../../images/foci_1_300.png
+   :width: 100%
+
+.. |pic3| image:: ../../images/intranuclear_1_300.png
+   :width: 100%
+
+.. |pic4| image:: ../../images/nuclear_edge_1_300.png
+   :width: 100%
+
+.. |pic5| image:: ../../images/perinuclear_1_300.png
+   :width: 100%
+
+.. |pic6| image:: ../../images/cell_edge_1_300.png
+   :width: 100%
+
+.. |pic7| image:: ../../images/protrusion_1_300.png
+   :width: 100%
+
 We build a map of probability distribution to bias the localization of
 generated spots. Maps are built from specific cell templates: