NLeSC · cantordust · Mar 17, 2026 · Mar 18, 2026 · Mar 18, 2026 · Mar 18, 2026
diff --git a/README.md b/README.md
@@ -1,11 +1,10 @@
-# modelCMT (cortical microtubule dynamics)
+# corticalsim3D (cortical microtubule dynamics)
 
-![alt text](https://github.com/HiBandan/modelCMT/blob/main/logo/logomodelCMT-3.0.png)
+![alt text](assets/logo/logomodelCMT-1.0.png)
 
+This is a program for simulating cortical microtubule dynamics (CMT) on experimentally extracted microscopic images of cell
 
-This is a program for simulating cortical microtubule dynamics (CMT) on experimentally extracted microscopic images of cell 
-
-Application: 
+Application:
 
 https://www.sciencedirect.com/science/article/pii/S0960982218309242
 
@@ -15,131 +14,90 @@ https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005959
 
 Testing and contributing is very welcome, especially if you can contribute with new algorithms and features.
 
-## WINDOWS
-
-  ### install gcc/g++ 
-
-  download Mingw: https://nuwen.net/mingw.html
-
-      run mingw-xx.exe -> this will create a folder MinGw
-
-      copy MinGw to C:\
-
-      add environment variable: C:\MinGW or C:\MinGW\bin
-
-  ### install eigen:
-
-  download eigen: https://drive.google.com/file/d/1VFLlKJI9EaSP9VUaeV8vmPQYkqdIIJPg/view?usp=sharing
-
-      extract "eigen-3.4.0" folder and rename it to "Eigen"
-
-      copy "Eigen" folder to C:\Program Files 
-
-  ### install boost:
-
-  download boost: https://drive.google.com/file/d/1apu5_am2kJj7HvXJNPhn30k_ryi3gJDf/view?usp=sharing
-
-      extract "boost_1_77_0" folder and rename it to "Boost"
-
-      copy "Boost" to C:\Program Files 
-
-  ### get the source code
-
-  Option 1: Download the package from the Github: https://github.com/HiBandan/modelCMT/archive/refs/heads/main.zip
-
-
-  Option 2: Clone from terminal: 
-
-    git clone https://github.com/HiBandan/modelCMT.git
-
-  ### install Code::Blocks: 
-  https://code-blocks.en.uptodown.com/windows
-
-  ### run 
-
-    open (with Code::Blocks): modelCMT_WINDOWS.cbp
-
-    Projects -> modelCMT.cbp -> add files
-        -> modules/cppFiles (all files except 'inline.cpp')
-        -> modules/headFiles (all files)
-        -> modules/paramFiles (all files)
-
-    settings -> compiler -> search directories (compiler) -> add 
-
-        -> C:\Program Files\Eigen 
-        -> C:\Program Files\Boost 
-
-    project -> 
-
-      set program’s arguments: ./modules/paramFiles/parameters_ARRAY.txt
-      build options -> search directories -> compiler -> add -> modules/cppFiles 
-      build options -> search directories -> compiler -> add -> modules/headFiles
-      build options -> linker settings -> add -> boost_system
-      build options -> linker settings -> add -> boost_filesystem
-      build options -> linker settings -> add -> libboost_filesystem
-
-    run 
-
-## LINUX
-
-  ### install gcc/g++ 
-
-       sudo apt update
-       sudo apt install build-essential
-
-  ### install eigen:
-
-  download eigen: https://drive.google.com/file/d/1VFLlKJI9EaSP9VUaeV8vmPQYkqdIIJPg/view?usp=sharing
-
-      extract "eigen-3.4.0" folder and rename it to "Eigen"
-
-      copy "Eigen" folder to /usr/local/include
-
-  ### install boost:
-
-  download boost: https://drive.google.com/file/d/1apu5_am2kJj7HvXJNPhn30k_ryi3gJDf/view?usp=sharing
-
-      extract "boost_1_77_0" folder and rename it to "Boost"
-
-      copy "Boost" to /usr/local/include
-
-  ### get the source code
-
-  Option 1: Download the package from the Github: https://github.com/HiBandan/modelCMT/archive/refs/heads/main.zip
-
-  Option 2: Clone from terminal: 
-
-    git clone https://github.com/HiBandan/modelCMT.git
-
-  ### install Code::Blocks: 
-
-  sudo add-apt-repository ppa:damien-moore/codeblocks-stable
-
-  sudo apt update
-
-  sudo apt install codeblocks codeblocks-contrib
-
-  ### run 
-
-    open (with code-block): modelCMT_LINUX.cbp
-
-    Projects -> modelCMT.cbp -> add files
-      -> modules/cppFiles (all files except 'inline.cpp')
-      -> modules/headFiles (all files)
-      -> modules/paramFiles (all files)
-
-    settings -> compiler -> search directories (compiler) -> add 
-
-        -> /usr/local/include/Eigen
-        -> /usr/local/include/Boost 
-
-    project -> 
-
-      set program’s arguments: ./modules/paramFiles/parameters_ARRAY.txt
-      build options -> search directories -> compiler -> add -> modules/cppFiles 
-      build options -> search directories -> compiler -> add -> modules/headFiles
-      build options -> linker settings -> add -> boost_system
-      build options -> linker settings -> add -> boost_filesystem
-      build options -> linker settings -> add -> libboost_filesystem
-
-    run 
+# Installation
+
+NOTE: You need a compiler that supports the C++ 14 standard as a minimum.
+
+## Install the dependencies
+
+`corticalsim3D` depends on Eigen and Boost (however, the latter will be dropped soon). In addition, you will need [Meson](https://mesonbuild.com/index.html) to build the executables, as well as a fairly recent C++ compiler (GCC or Clang) supporting the C++ 14 standard. The following instructions outline the process of installing the dependencies on different platforms, as well as compiling and installing the `corticalsim3D` package itself.
+
+### Windows
+
+Most dependencies need to be installed manually on Windows.
+
+1. GCC
+
+    1. Download [MinGW](https://www.mingw-w64.org/)
+    1. Run `mingw-xx.exe` (this will create a folder called `MinGw`)
+    1. Copy the `MinGw` folder to `C:\`
+    1. Add `C:\MinGW` and `C:\MinGW\bin` to the system path
+
+1. Eigen
+
+    1. Download [Eigen](https://libeigen.gitlab.io/)
+    1. Extract `eigen-3.4.0` folder and rename it to `Eigen`
+    1. Copy the `Eigen` folder to `C:\Program Files`
+
+1. Boost
+
+    Download and install [Boost](https://www.boost.org/releases/latest/).
+
+    <span style="color: red;">NOTE</span>: The Boost dependency will be deprecated and removed soon.
+
+1. Meson
+
+    Use the official [Meson installer for Windows](https://github.com/mesonbuild/meson/releases). The installer also bundles the Ninja dependency, so you don't have to install that separately.
+
+### Linux
+
+Please use your package manager to install all the dependencies. Most Linux distributions provide packages for GCC, Meson, Ninja, Boost and Eigen.
+
+Instructions for Ubuntu (*to be confirmed, may be incomplete*):
+
+```bash
+sudo apt update && apt upgrade
+sudo apt install gcc libboost-all-dev libeigen3-dev meson ninja-build
+```
+
+## Compile
+
+1. First, clone the `corticalsim3D` repository:
+
+    ```bash
+    git clone https://github.com/NLeSC/corticalsim3D
+    ```
+
+    NOTE: It is recommended that you do **_not_** enter the `corticalsim3D` directory. The next steps assume an out-of-source build setup, meaning that the directory (where the package will be compiled) will be outside the source tree. This has several advantages, such as precluding the possibility of accidentally committing build artefacts to the repository.
+
+1. Configure the build with `meson`:
+
+    ```bash
+    meson setup build corticalsim3D
+    ```
+
+    This command uses the Meson build system to bootstrap everything that we need for the compilation into a directory called `build` from the sources located in the `corticalsim3D` directory.
+
+1. Enter the build directory and compile the source:
+
+    ```bash
+    cd build
+    meson compile
+    ```
+
+    This will generate an executable file called `corticalsim3D` in the current directory (`build`).
+
+## Run
+
+Run the `corticalsim3D` executable with a parameter file as the first argument. Two example parameter files are provided in the `corticalsim3D/config` directory: `parameters_ARRAY.txt` and `parameters_FLY.txt`. The
+
+```bash
+./corticalsim3d ../corticalsim3D/config/parameters_ARRAY.txt
+```
+
+# TODO
+
+- [ ] Reproduce the installation instructions for Windows and update them as necessary.
+- [ ] Add specific installation instructions for dependencies for different Linux distributions (Ubuntu, Debian, Arch...).
+- [ ] Add installation instructions for MacOSX.
+- [ ] Meson: Option to install the executable into a custom directory
diff --git a/config/modelCMT_LINUX.cbp b/config/modelCMT_LINUX.cbp
diff --git a/config/modelCMT_WINDOWS.cbp b/config/modelCMT_WINDOWS.cbp
diff --git a/config/parameters_ARRAY.txt b/config/parameters_ARRAY.txt
@@ -1,8 +1,8 @@
 #########################
 ### Input-Output path ###
 #########################
-inputDir 	./inputData
-outputDir 	./inputData
+inputDir 	../corticalsim3D/data
+outputDir 	../corticalsim3D/data
 createSubdir 0
 ##################################
 ### changing parameters on fly ###

diff --git a/meson.build b/meson.build
@@ -0,0 +1,17 @@
+project('corticalsim', 'cpp')
+
+# Compiler flags
+# add_global_arguments('-O2', language : 'cpp')
+
+# Directories containing header files
+incdir = include_directories('include')
+
+# Directories containing source files
+subdir('src')
+
+# Dependencies
+eigen = dependency('Eigen3', modules: ['Eigen3::Eigen'])
+boost = dependency('boost', modules : ['filesystem'])
+
+# Executable(s)
+executable('corticalsim3d', sources, include_directories: incdir, dependencies: [eigen, boost])
diff --git a/src/meson.build b/src/meson.build
@@ -0,0 +1,12 @@
+sources = files('eig3.cpp',
+    'IO-analysis.cpp',
+    'meshImport.cpp',
+    'parameters.cpp',
+    'queue.cpp',
+    'microtubule.cpp',
+    'system.cpp',
+    'geometry-generic.cpp',
+    'geometry-special.cpp',
+    'main.cpp'
+)
+