Add explanation on example images and models. Now we have both 2D and…

… 3D images and models.

README.md

@@ -40,7 +40,29 @@ available as an [MP4 file](./screenshots/example1.mp4)).
 
 ![example1](./screenshots/example1.gif "Convert segmented images to Spatial SBML")
 
-You can find example 2D and 3D images and converted Spatial SBML model under [examples](https://github.com/spatialsimulator/XitoSBML/tree/master/examples) directory.
+### Example files
+This repository also contains example 2D and 3D images and converted Spatial
+SBML models under [examples](https://github.com/spatialsimulator/XitoSBML/tree/master/examples) directory.
+Here is a description on example files.
+
+#### 2D images and model
+directory | filename | input or output | description
+:-- | :--|:--:|:--
+`examples/2D` | `Rat_Hippocampal_Neuron-Nuc.tiff` | input | 2D segmented image of nucleus
+`examples/2D` | `Rat_Hippocampal_Neuron-Cyt.tiff` | input | 2D segmented image of cytosol
+`examples/2D` | `example2D.xml` | output | 2D spatial SBML model generated by XitoSBML
+`examples/2D` | `example2D.tiff` | output | 2D merged segmented image generated by XitoSBML
+`examples/2D` | `Rat_Hippocampal_Neuron-Hoechst.tiff` | -- | Original 2D fluroscent microscopic image of nucleus
+`examples/2D` | `Rat_Hippocampal_Neuron-NicotinicAcetylcholineAlpha7.tiff` | -- | Original 2D fluroscent microscopic image of cytosol
+
+#### 3D images and model
+
+directory | filename | input or output | description
+:-- | :--|:--:|:--
+`examples/3D` | `nuc-zstack.tiff` | input | 3D (Z-stack) segmented image of nucleus
+`examples/3D` | `cyt-zstack.tiff` | input | 3D (Z-stack) segmented image of cytosol
+`examples/3D` | `zstack.xml` | output | 3D spatial SBML model generated by XitoSBML
+`examples/3D` | `zstack.tiff` | output | 3D (Z-stack) merged segmented image generated by XitoSBML
 
 ### Convert segmented (binary) images to Spatial SBML (as a mathematical model)
 Next example will show how to create a Spatial SBML model, add SBML objects to the model, and make it as a mathematical model. The following figure represents the diagram of this example model. Note that species `A` and `B` diffuse inside the nucleus and cytosol with the given diffusion coefficients (`Dnuc` and `Dcyt`), respectively.
@@ -71,15 +93,15 @@ The mathematical (spatial) model created by this example can be executed by seve
 ```sh
 git clone https://github.com/funasoul/docker-spatialsim.git
 cd ./docker-spatialsim/
-# Copy example2.xml to this directory
-./docker-spatialsim.sh -t 0.2 -d 0.0001 -o 50 example2.xml
+# Copy example2D.xml to this directory
+./docker-spatialsim.sh -t 0.2 -d 0.0001 -o 50 example2D.xml
 ```
 
 SpatialSimulator will generate numbers and images of the simulation result.
 
 Species A             |  Species B
 :-------------------------:|:-------------------------:
-![example2 species A](./screenshots/example2_a.gif "Simulation result of example2.xml (species A)") | ![example2 species B](./screenshots/example2_b.gif "Simulation result of example2.xml (species B)")
+![example2 species A](./screenshots/example2_a.gif "Simulation result of example2D.xml (species A)") | ![example2 species B](./screenshots/example2_b.gif "Simulation result of example2D.xml (species B)")
 
 How to Compile
 ------------------
@@ -104,7 +126,7 @@ For example, if you want to build XitoSBML on Fiji.app(MacOSX), the `mvn` comman
 ```
 
 ### Documentation
-Javadocs of XitoSBML API are included under `apidocs` directory in the repository, and 
+Javadocs of XitoSBML API are included under `apidocs` directory in the repository, and
 are available on our [web site](https://fun.bio.keio.ac.jp/software/XitoSBML/apidocs/).
 
 Here are the high-level key classes of XitoSBML, which will be a good starting point to read through the code.