diff --git a/conda/apptainer.def b/conda/apptainer.def
new file mode 100644
index 00000000..41235c77
--- /dev/null
+++ b/conda/apptainer.def
@@ -0,0 +1,16 @@
+Bootstrap: docker
+From: ubuntu:22.04
+
+%environment
+    export HOME=/casa/home
+
+%post
+    mkdir /casa
+    apt update
+
+%runscript
+    echo "Start casa container"
+    export PATH=/casa/conda/bin:$PATH
+    export LD_LIBRARY_PATH=/casa/conda/lib:$LD_LIBRARY_PATH
+
+    exec "$@"
diff --git a/conda/setup_conda b/conda/setup_conda
index cf090bf7..878f4f72 100755
--- a/conda/setup_conda
+++ b/conda/setup_conda
@@ -4,6 +4,7 @@ set -e
 set -x
 
 casaconda="$1"
+script_dir=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
 
 if [ -z "$casaconda" ]; then
     echo "Missing destination directory"
@@ -14,141 +15,43 @@ if [ ! -e "$casaconda" ]; then
     mkdir "$casaconda"
 fi
 
+if [ ! -e "$casaconda/home" ]; then
+    mkdir "$casaconda/home"
+    for f in .gitconfig .git-credentials; do
+        if [ -e "$HOME/$f" ]; then
+            cp "$HOME/$f" "$casaconda/home"
+        fi
+    done
+fi
+
 system_image="$casaconda/system"
 if [ ! -e "$system_image" ]; then
-    apptainer build --sandbox --disable-cache "$casaconda/system" docker://ubuntu:22.04
-    apptainer run --fakeroot --writable "$system_image" mkdir /conda
-    apptainer run --fakeroot --writable "$system_image" apt update
+    apptainer build --sandbox "$casaconda/system" "$script_dir/apptainer.def"
 fi
 
 if [ ! -e "$casaconda/Miniforge3-Linux-x86_64.sh" ]; then
     wget -O "$casaconda/Miniforge3-Linux-x86_64.sh" https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh
 fi
 
-apptainer="apptainer run -B $casaconda/conda:/conda $system_image"
-conda="$apptainer /conda/bin/conda"
+apptainer="apptainer run --containall $mounts-B $casaconda:/casa -B /tmp $system_image"
+root_apptainer="apptainer run --writable --fakeroot --containall -B $casaconda:/casa -B /tmp $system_image"
+
+conda="$apptainer /casa/conda/bin/conda"
 if [ ! -e "$casaconda/conda" ]; then
     mkdir "$casaconda/conda"
-    cd "$casaconda"
-    apptainer run -B "$casaconda/conda:/conda" "$system_image" sh "./Miniforge3-Linux-x86_64.sh" -u -b -p "/conda"
+    $apptainer sh "/casa/Miniforge3-Linux-x86_64.sh" -u -b -p "/casa/conda"
     $conda update conda -y
 fi
 
-script_dir=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
-
-cp -a "$script_dir/setup_run_apt" "$casaconda/conda/"
-apptainer run --fakeroot --writable -B $casaconda/conda:/conda "$system_image" /conda/setup_run_apt
-
-cp -a "$script_dir/setup_run_conda" "$casaconda/conda/"
-$apptainer /conda/setup_run_conda
+for script in setup_run_apt setup_run_conda setup_run_compiled; do
+    cp -a "$script_dir/$script" "$casaconda"
+    $root_apptainer /casa/$script
+done
 
-#
-#  Dev environment
-#
-
-# Source version control
-version_control_packages=(
-    git
-    git-lfs
-    #! git-man
-    #! subversion still necessary ?
-)
-
-# Configure/build toolchain
-toolchain_packages=(
-    automake
-    clang
-    cmake
-    #! cmake-curses-gui
-    gxx
-    gcc
-    gfortran
-    #! libc-dev
-    make
-    pkg-config
-    #! pyqt5-dev
-    #! pyqt5-dev-tools
-    #! python3-sip-dev
-    #! qtchooser
-)
-
-# Development tools and convenience utilities
-development_tools=(
-    ack-grep
-    bash-completion
-    emacs-nox
-    flake8
-    gdb
-    gdbserver
-    valgrind
-    gedit
-    git-man
-    gitg
-    gitk
-    kate
-    kdiff3
-    kompare
-    kwrite
-    locate
-    meld
-    nano
-    python2  # only for flake8 tests of casa-distro
-    python3-autopep8
-    python3-objgraph
-    python3-venv
-    spyder
-    strace
-    tox
-    vim
-    xterm
-    xdot
-)
-
-# Documentation building
-documentation_building_packages=(
-    doxygen
-    ghostscript
-    graphviz
-    nbconvert #? was jupyter-nbconvert
-    pandoc
-    sphinx
-    sphinx-gallery
-    #! texlive-latex-base
-    #! texlive-latex-extra  # needed by doxygen to render LaTeX formulas
-    #! texlive-fonts-recommended
-    wkhtmltopdf
-)
-
-brainvisa_standard_dev_dependencies=(
-    #! libasound2-dev
-    libblitz #? was libblitz0-dev
-    boost-cpp #? was libboost-dev
-    #! libboost-filesystem-dev
-    #! libboost-system-dev
-    dcmtk #? was libdcmtk-dev
-    libexpat #? was libexpat1-dev
-    #! libgl1-mesa-dev
-    libglib #? was libglib2.0-dev
-    libglu #? was libglu1-mesa-dev
-    libjpeg-turbo #? was libjpeg-dev
-    #! libminc-dev
-    netcdf4 #? was libnetcdf-dev
-    #! libomp-dev  # OpenMP with the clang compiler
-    #! libopenjp2-7-dev
-    libpng #? was libpng-dev
-    #! libqt5x11extras5-dev
-    #! libqwt-qt5-dev
-    libsigcpp #? was libsigc++-2.0-dev
-    #! libspnav-dev
-    libsvm #? was libsvm-dev
-    libtiff #? was libtiff-dev
-    #! libvtk9-dev
-    #! libvtk9-qt-dev
-    libxml2 #? was libxml2-dev
-    #! qttools5-dev
-    #! qtmultimedia5-dev
-    #! qttools5-dev-tools
-    #! zlib1g-dev
-)
+if [ ! -e "$casaconda/src" ]; then
+    $apptainer git clone https://github.com/sapetnioc/brainvisa-submodules /casa/src
+    $apptainer git -C /casa/src submodule update --init --recursive
+fi
 
-"$conda" install -y ${version_control_packages[@]} ${toolchain_packages[@]} ${documentation_building_packages[@]} ${brainvisa_standard_dev_dependencies[@]}
+# Update all sources
+$apptainer git -C /casa/src submodule foreach ls
diff --git a/conda/setup_dev_conda b/conda/setup_dev_conda
new file mode 100755
index 00000000..1fe8e495
--- /dev/null
+++ b/conda/setup_dev_conda
@@ -0,0 +1,124 @@
+#! /bin/bash
+
+#
+# Setup dev dependencies with conda
+#
+
+set -x
+set -e
+
+conda=/casa/conda/bin/conda
+
+if [ -e /casa/conda/bin/nano ]; then
+    # if nano is installed, we assume that this script has already been
+    # executed.
+    echo "setup_dev_conda already executed => execution canceled"
+    exit 0
+fi
+
+# Source version control
+version_control_packages=(
+    git
+    git-lfs
+    #! git-man
+    #! subversion still necessary ?
+)
+
+# Configure/build toolchain
+toolchain_packages=(
+    automake
+    clang
+    cmake
+    #! cmake-curses-gui
+    gxx
+    gcc
+    gfortran
+    #! libc-dev
+    make
+    pkg-config
+    #! pyqt5-dev
+    #! pyqt5-dev-tools
+    #! python3-sip-dev
+    #! qtchooser
+)
+
+# Development tools and convenience utilities
+development_tools=(
+    ack-grep
+    bash-completion
+    emacs-nox
+    flake8
+    gdb
+    gdbserver
+    valgrind
+    gedit
+    git-man
+    gitg
+    gitk
+    kate
+    kdiff3
+    kompare
+    kwrite
+    locate
+    meld
+    nano
+    python2  # only for flake8 tests of casa-distro
+    python3-autopep8
+    python3-objgraph
+    python3-venv
+    spyder
+    strace
+    tox
+    vim
+    xterm
+    xdot
+)
+
+# Documentation building
+documentation_building_packages=(
+    doxygen
+    ghostscript
+    graphviz
+    nbconvert #? was jupyter-nbconvert
+    pandoc
+    sphinx
+    sphinx-gallery
+    #! texlive-latex-base
+    #! texlive-latex-extra  # needed by doxygen to render LaTeX formulas
+    #! texlive-fonts-recommended
+    wkhtmltopdf
+)
+
+brainvisa_standard_dev_dependencies=(
+    #! libasound2-dev
+    libblitz #? was libblitz0-dev
+    boost-cpp #? was libboost-dev
+    #! libboost-filesystem-dev
+    #! libboost-system-dev
+    dcmtk #? was libdcmtk-dev
+    libexpat #? was libexpat1-dev
+    #! libgl1-mesa-dev
+    libglib #? was libglib2.0-dev
+    libglu #? was libglu1-mesa-dev
+    libjpeg-turbo #? was libjpeg-dev
+    #! libminc-dev
+    netcdf4 #? was libnetcdf-dev
+    #! libomp-dev  # OpenMP with the clang compiler
+    #! libopenjp2-7-dev
+    libpng #? was libpng-dev
+    #! libqt5x11extras5-dev
+    #! libqwt-qt5-dev
+    libsigcpp #? was libsigc++-2.0-dev
+    #! libspnav-dev
+    libsvm #? was libsvm-dev
+    libtiff #? was libtiff-dev
+    #! libvtk9-dev
+    #! libvtk9-qt-dev
+    libxml2 #? was libxml2-dev
+    #! qttools5-dev
+    #! qtmultimedia5-dev
+    #! qttools5-dev-tools
+    #! zlib1g-dev
+)
+
+$conda install -y ${version_control_packages[@]} ${toolchain_packages[@]} ${documentation_building_packages[@]} ${brainvisa_standard_dev_dependencies[@]}
diff --git a/conda/setup_run_compiled b/conda/setup_run_compiled
new file mode 100755
index 00000000..815c314c
--- /dev/null
+++ b/conda/setup_run_compiled
@@ -0,0 +1,51 @@
+#! /bin/bash
+
+#
+# Setup run dependencies requiring software compilation
+#
+
+set -x
+set -e
+
+if [ -e /casa/conda/lib/pkgconfig/libopenjp2.pc ]; then
+    # if libopenjp2.pc is installed, we assume that this script has already been
+    # executed.
+    echo "setup_run_compiled already executed => execution canceled"
+    exit 0
+fi
+
+# MIRCen's fork of openslide with support for CZI format
+#
+tmp=$(mktemp -d)
+
+cd "$tmp"
+wget https://github.com/uclouvain/openjpeg/archive/refs/tags/v2.5.0.tar.gz
+tar xf v2.5.0.tar.gz
+cd openjpeg-2.5.0
+mkdir build
+cd build
+cmake .. -DCMAKE_BUILD_TYPE=Release "-DCMAKE_INSTALL_PREFIX=/casa/conda"
+make
+make install
+cp libopenjp2.pc /casa/conda/lib/pkgconfig/
+
+cd "$tmp"
+git clone --depth=1 https://github.com/MIRCen/openslide.git
+cd openslide
+autoreconf --install
+./configure --prefix="/casa/conda"
+make -j$(nproc)
+make install
+
+# reinstall libminc 4.0.0 because newer versions can't properly read freesurfer
+# .mgz files
+cd "$tmp"
+git clone https://github.com/BIC-MNI/libminc.git --single-branch --branch libminc-2-3-00
+cd libminc
+cmake . -DBUILD_TESTING=OFF -DCMAKE_BUILD_TYPE=Release -DLIBMINC_BUILD_SHARED_LIBS=ON -DLIBMINC_MINC1_SUPPORT=ON "-DCMAKE_INSTALL_PREFIX=/casa/conda"
+make -j$(nproc)
+make install
+cd ..
+rm -rf libminc
+
+rm -Rf "$tmp"
diff --git a/conda/setup_run_conda b/conda/setup_run_conda
index 0d2bf8cd..607e4091 100755
--- a/conda/setup_run_conda
+++ b/conda/setup_run_conda
@@ -7,7 +7,14 @@
 set -x
 set -e
 
-conda=/conda/bin/conda
+if [ -e /casa/conda/bin/git ]; then
+    # if git is installed, we assume that this script has already been
+    # executed.
+    echo "setup_run_conda already executed => execution canceled"
+    exit 0
+fi
+
+conda=/casa/conda/bin/conda
 
 build_dependencies=(
     # General build dependencies (notably useful for pip-compiled packages)
@@ -121,45 +128,6 @@ headless_anatomist_dependencies=(
 
 $conda install -y ${build_dependencies[@]} ${fsl_runtime_dependencies[@]} ${matlab_runtime_dependencies[@]} ${generally_useful_packages[@]} ${headless_anatomist_dependencies[@]}
 
-export PATH="/conda/bin:$PATH"
-export LD_LIBRARY_PATH="/conda/lib:$LD_LIBRARY_PATH"
-
-# MIRCen's fork of openslide with support for CZI format
-#
-tmp=$(mktemp -d)
-
-cd "$tmp"
-wget https://github.com/uclouvain/openjpeg/archive/refs/tags/v2.5.0.tar.gz
-tar xf v2.5.0.tar.gz
-cd openjpeg-2.5.0
-mkdir build
-cd build
-cmake .. -DCMAKE_BUILD_TYPE=Release "-DCMAKE_INSTALL_PREFIX=/conda"
-make
-make install
-cp libopenjp2.pc /conda/lib/pkgconfig/
-
-cd "$tmp"
-git clone --depth=1 https://github.com/MIRCen/openslide.git
-cd openslide
-autoreconf --install
-./configure --prefix="/conda"
-make -j$(nproc)
-make install
-
-# reinstall libminc 4.0.0 because newer versions can't properly read freesurfer
-# .mgz files
-cd "$tmp"
-git clone https://github.com/BIC-MNI/libminc.git --single-branch --branch libminc-2-3-00
-cd libminc
-cmake . -DBUILD_TESTING=OFF -DCMAKE_BUILD_TYPE=Release -DLIBMINC_BUILD_SHARED_LIBS=ON -DLIBMINC_MINC1_SUPPORT=ON "-DCMAKE_INSTALL_PREFIX=/conda"
-make -j$(nproc)
-make install
-cd ..
-rm -rf libminc
-
-rm -Rf "$tmp"
-
 
 pip_installed_dependencies=(
     'pydantic>=1.9'