diff --git a/.ai/context.md b/.ai/context.md
new file mode 100644
index 00000000..4d11452f
--- /dev/null
+++ b/.ai/context.md
@@ -0,0 +1,399 @@
+# ReproStim Project AI Context/Memory File
+
+## Project Overview
+
+**ReproStim** is a comprehensive video capture and recording suite designed for neuroimaging and psychology experiments. It provides experimenters with a complete, high-fidelity audio-visual record of stimulus presentation during fMRI scanning sessions as part of the **ReproFlow** ecosystem for reproducible neuroimaging data collection.
+
+### Core Mission
+- Automatic capture of all audio/video stimuli presented to research subjects
+- Integration with BIDS (Brain Imaging Data Structure) datasets
+- Minimal effort required from end-users (runs silently in background)
+- Enhanced experimental reproducibility and data loss prevention
+- Recovery of experimental data in case of irregularities or scanner glitches
+
+### Architecture Overview
+```
+Hardware Layer (Magewell USB Capture Device)
+          ↓
+Capture Services (C++ videocapture/screencapture)
+          ↓
+Python Analysis Tools (QR parsing, audio codes, video audit)
+          ↓
+BIDS Integration & Documentation
+```
+
+## Project Structure
+
+### Main Directories
+
+#### `src/reprostim/` - Python Package (Core)
+Main Python package with CLI tools and analysis utilities.
+
+**Key Modules:**
+- **cli/** - Command-line interface (Click-based with DYMGroup for suggestions)
+  - `entrypoint.py` - Main CLI dispatcher
+  - `cmd_qr_parse.py` - Parse QR codes from `.mkv` videos (PARSE/INFO modes)
+  - `cmd_timesync_stimuli.py` - PsychoPy integration for QR/audio code generation
+  - `cmd_detect_noscreen.py` - Detect no-signal/rainbow frames with fixup capabilities
+  - `cmd_list_displays.py` - List available GUI displays (cross-platform)
+  - `cmd_monitor_displays.py` - Monitor display connection status with callbacks
+  - `cmd_video_audit.py` - Comprehensive video analysis (incremental/full/force modes)
+  - `cmd_echo.py` - Simple echo command for testing
+
+- **qr/** - QR code processing and time synchronization
+  - `qr_parse.py` - Parse `.mkv` files, extract QR codes, audio codes, metadata → JSONL
+  - `timesync_stimuli.py` - PsychoPy-based MRI/BIRCH/Magewell synchronization
+  - `disp_mon.py` - Cross-platform display monitoring (Linux/macOS/Windows)
+  - `psychopy.py` - PsychoPy framework integration utilities
+  - `video_audit.py` - Comprehensive video analysis with multiple audit sources
+
+- **audio/** - Audio codec generation
+  - `audiocodes.py` - FSK/NFE codecs with Reed-Solomon error correction
+  - Supports PsychoPy audio backends (sounddevice, PTB)
+  - CRC8 checksum implementation for data validation
+
+- **capture/** - Video capture utilities
+  - `nosignal.py` - Rainbow/no-signal frame detection (multi-algorithm: has_rainbow, has_rainbow2)
+  - VideoInfo Pydantic model for structured metadata
+  - Video fixup capabilities using ffmpeg for truncated/invalid-timing videos
+
+#### `src/reprostim-capture/` - C++ Video Capture Suite
+CMake-based C++ project with 3 main executables.
+
+**Structure:**
+```
+src/reprostim-capture/
+├── CMakeLists.txt           # Main build configuration (C++20)
+├── capturelib/              # Core capture library
+│   ├── include/reprostim/   # Headers (CaptureLib, CaptureLog, CaptureApp)
+│   ├── src/                 # Implementation files
+│   └── test/                # Catch2-based C++ tests
+├── screencapture/           # Screen capture utility
+├── videocapture/            # Magewell USB video capture
+├── rectrigger/              # Trigger server/client
+└── 3rdparty/                # Magewell SDK (versions 3.3.1.0 and 3.3.1.1313)
+```
+
+**Key Components:**
+- **CaptureLib**: Core library with threading, REST API, ReproMon integration, logging
+- **ScreenCapture**: Desktop/screen recording utility
+- **VideoCapture**: Magewell USB device capture with configuration support
+- **Dependencies**: libMWCapture (Magewell SDK), libusb, wxWidgets, portaudio
+
+#### `tests/` - Test Suite
+```
+tests/
+├── audio/
+│   └── test_audiocodes.py   # Audio codec tests (CRC8)
+└── data/
+    ├── reprostim-videos/    # Test video samples
+    └── nosignal/            # No-signal detection test data
+```
+
+**Testing Approach:**
+- **Python**: pytest with pytest-cov (coverage), pytest-mock (mocking), pytest-xdist (parallel)
+- **C++**: Catch2 framework (v2/v3 compatible)
+- **CI/CD**: GitHub Actions workflows, container-based integration tests
+
+#### `docs/` - Documentation
+Sphinx + MyST (Markdown support) documentation.
+
+**Structure:**
+```
+docs/source/
+├── conf.py              # Sphinx configuration
+├── index.rst            # Main documentation index
+├── intro/               # Introduction docs
+├── install/             # Installation guide (Markdown)
+├── cli/                 # CLI command documentation (auto-generated)
+├── api/                 # Auto-generated API reference
+├── dev/                 # Development guide
+├── notes/               # Technical notes (disp_mon, psychopy, VAAPI, ffmpeg)
+├── changes/             # Changelog/release notes
+└── _static/             # Static assets
+```
+
+**Special Features:**
+- Auto-documentation via sphinx-click
+- Mermaid diagram support
+- Read the Docs integration (`.readthedocs.yaml`)
+- SVG-based ReproFlow diagram
+- Platform-specific notes (Linux, macOS, Windows)
+
+#### `containers/` - Container Definitions
+Docker and Singularity container support for deployment.
+
+**Structure:**
+```
+containers/repronim-reprostim/
+├── Dockerfile.repronim-reprostim
+├── Singularity.repronim-reprostim
+├── generate_container.sh    # Template generation
+├── build_docker.sh
+├── build_singularity.sh
+├── run_reprostim.sh
+├── build_reprostim.sh       # Install script (PsychoPy + reprostim)
+└── README.md
+```
+
+**Container Strategy:**
+- **Base**: Neurodebian (bookworm)
+- **PsychoPy**: Version 2025.2.0 via psychopy_linux_installer
+- **Python**: 3.10 with all optional dependencies
+- **Modes**: CI/CD mode (install from worktree) vs default mode (install from PyPI)
+- **Features**: Development overlay support for debugging
+
+#### `tools/` - CI/CD and Configuration Scripts
+```
+tools/
+├── ci/                      # CI/CD scripts
+│   ├── build_reprostim_container.sh
+│   ├── run_reprostim_container.sh
+│   ├── test_reprostim_container.sh
+│   ├── test_reprostim_timesync-stimuli.sh
+│   └── test_reprostim_events.sh
+└── reproiner-config.sh      # ReproInner configuration
+```
+
+## Technology Stack
+
+### Python Dependencies
+- **Click 8.1.7+**: CLI framework with did-you-mean suggestions
+- **PsychoPy**: Psychology experiment framework (optional)
+- **OpenCV (cv2) 4.9.0+**: Video processing and QR code detection
+- **Pyzbar 0.1.9+**: QR code scanning
+- **Pydantic 2.7.1+**: Data validation and serialization
+- **Numpy 1.26.4+**: Numerical operations
+- **SciPy 1.14.1+**: Signal processing
+- **sounddevice 0.5.1+**: Audio I/O
+- **pygame 2.6.1+**: Display monitoring
+- **PyAudio 0.2.14+**: Audio interface
+- **reedsolo 1.7.0+**: Reed-Solomon error correction
+- **psutil**: System monitoring
+
+### C++ Stack
+- **C++20**: Modern C++ standard
+- **CMake 3.10+**: Build system
+- **Magewell SDK 3.3.1**: USB capture device API
+- **Catch2**: C++ testing framework (v2/v3)
+- **libusb**: USB device interaction
+
+### Documentation & Testing
+- **Sphinx + MyST**: Documentation generation
+- **pytest**: Python testing framework
+- **pytest-cov**: Code coverage
+- **pytest-mock**: Test mocking
+- **pytest-xdist**: Parallel test execution
+
+## Installation Options
+
+```bash
+# Core package
+pip install reprostim
+
+# With audio codec support
+pip install reprostim[audio]
+
+# With display monitoring (platform-specific)
+pip install reprostim[disp_mon]
+
+# With PsychoPy integration
+pip install reprostim[psychopy]
+
+# Everything
+pip install reprostim[all,disp_mon]
+```
+
+## Build Systems
+
+### Python Package
+```bash
+# Build system: hatchling with versioningit
+# Version source: Git tags → src/reprostim/_version.py
+# Distribution: PyPI (reprostim) and Conda-Forge
+
+pip install -e .
+```
+
+### C++ Build
+```bash
+cd src/reprostim-capture
+mkdir build && cd build
+cmake .. -DCTEST_ENABLED=ON
+make
+make test
+sudo make install  # Installs to CMAKE_INSTALL_PREFIX/bin
+```
+
+### Container Build
+```bash
+cd containers/repronim-reprostim
+./generate_container.sh
+./build_docker.sh
+# or
+./build_singularity.sh
+```
+
+## Workflow and Data Flow
+
+```
+Live Experiment Session
+    ↓
+Magewell USB Capture Device (Hardware)
+    ↓
+reprostim-videocapture (C++) → Records .mkv videos
+    ↓
+reprostim timesync-stimuli (Python/PsychoPy)
+    ├─ Generates QR codes on screen (video)
+    └─ Generates audio codes (FSK/NFE)
+    ↓
+Recorded Videos contain: Video + QR codes + Audio codes
+    ↓
+reprostim qr-parse → Extract QR/audio metadata (JSONL)
+    ↓
+reprostim video-audit → Analyze all videos, generate videos.tsv
+    ↓
+reprostim detect-noscreen → Check for no-signal frames
+    ↓
+Integrated with BIDS datasets for archival
+```
+
+## Important Files
+
+| File | Purpose |
+|------|---------|
+| `pyproject.toml` | Python package configuration, dependencies, build metadata |
+| `CMakeLists.txt` | C++ build configuration (reprostim-capture) |
+| `README.md` | Project overview, quick start guide |
+| `CHANGELOG.md` | Release notes and version history |
+| `overview.md` | Detailed project scope and architecture |
+| `src/reprostim/__init__.py` | Logger initialization, package entry point |
+| `src/reprostim/cli/entrypoint.py` | Main CLI dispatcher |
+| `src/reprostim/qr/qr_parse.py` | Video QR code extraction (JSONL output) |
+| `src/reprostim/audio/audiocodes.py` | FSK/NFE audio codec generation |
+| `src/reprostim/capture/nosignal.py` | No-signal frame detection algorithm |
+| `.readthedocs.yaml` | Read the Docs build configuration |
+| `.github/workflows/` | GitHub Actions CI/CD pipeline definitions |
+
+## Configuration Files
+
+| Config File | Role |
+|-------------|------|
+| `pyproject.toml` | Package metadata, dependencies, build backend (hatchling), tool configs |
+| `CMakeLists.txt` | C++ build configuration, compiler flags, dependencies |
+| `.readthedocs.yaml` | Read the Docs build environment, Python version |
+| `.pre-commit-config.yaml` | Pre-commit hooks for code quality |
+| `.codespellrc` | Spell checking configuration |
+| `REUSE.toml` | SPDX license compliance configuration |
+| `containers/*/Dockerfile*` | Container image definitions |
+| `src/reprostim-capture/version.txt` | Version string for C++ build |
+
+## Git Information
+
+- **Current Branch**: `enh-perms` (enhancement for permissions)
+- **Main Branch**: `master` (use for PRs)
+- **Recent Commits**: Focus on permissions fixes, container generation, QR/nosignal features
+- **License**: MIT
+- **Version**: 0.7.x (Alpha development status)
+
+## Team and Community
+
+- **Organization**: ReproNim (Reproducible Neuroimaging)
+- **Core Contributors**:
+  - Yaroslav Halchenko (lead)
+  - Vadim Melnik (active development)
+  - Horea Christian
+  - Andy Connolly
+- **Project Links**:
+  - GitHub: https://github.com/ReproNim/reprostim
+  - Documentation: Read the Docs (configured)
+  - PyPI: reprostim package
+
+## Development Guidelines
+
+### Code Quality
+- Pre-commit hooks configured (see `.pre-commit-config.yaml`)
+- Spell checking via codespell
+- SPDX license compliance (REUSE.toml)
+- Shellcheck for bash scripts (disable SC2086, SC2034 in build_reprostim.sh)
+
+### Testing
+- Run Python tests: `pytest tests/`
+- Run C++ tests: `cd build && make test`
+- CI tests: `tools/ci/test_reprostim_container.sh`
+
+### Documentation
+- Build docs: `cd docs && make html`
+- Auto-generated CLI docs via sphinx-click
+- Technical notes in `docs/source/notes/`
+
+### Version Management
+- Version source: Git tags
+- Auto-generated: `src/reprostim/_version.py` via versioningit
+- C++ version: `src/reprostim-capture/version.txt`
+
+## Common Tasks
+
+### Running CLI Commands
+```bash
+# Parse QR codes from video
+reprostim qr-parse video.mkv
+
+# Run PsychoPy time synchronization
+reprostim timesync-stimuli
+
+# Detect no-signal frames
+reprostim detect-noscreen video.mkv
+
+# Audit all videos
+reprostim video-audit /path/to/videos
+
+# List displays
+reprostim list-displays
+
+# Monitor displays
+reprostim monitor-displays
+```
+
+### Building Containers
+```bash
+cd containers/repronim-reprostim
+
+# Generate templates
+./generate_container.sh
+
+# Build Docker (default mode - PyPI install)
+./build_docker.sh
+
+# Build for CI (install from worktree)
+./build_docker.sh ci
+
+# Build Singularity
+./build_singularity.sh
+```
+
+### C++ Capture Tools
+```bash
+# After building and installing:
+reprostim-videocapture -V          # Check version
+reprostim-screencapture --help     # Screen capture help
+```
+
+## Notes and Caveats
+
+1. **PsychoPy Version**: Container uses 2025.2.0 (latest) with Python 3.10
+2. **Display Monitoring**: Platform-specific dependencies (pygame, pyglet, pyudev for Linux; quartz for macOS)
+3. **Magewell SDK**: 3rdparty directory contains SDK versions 3.3.1.0 and 3.3.1.1313
+4. **BIDS Integration**: Project designed to work within BIDS dataset structure
+5. **Permissions**: Recent work on `/opt` permissions (enh-perms branch)
+6. **Container Modes**: CI mode installs from worktree, default mode from PyPI
+
+## Recent Development Focus (from CHANGELOG)
+
+- Video audit tool creation
+- PsychoPy integration improvements
+- Container support (Docker/Singularity)
+- Display monitoring capabilities
+- Audio codec improvements (FSK/NFE)
+- Permissions fixes in container builds
+- QR code and nosignal detection enhancements
\ No newline at end of file
diff --git a/REUSE.toml b/REUSE.toml
index 45d9d7b0..6d798a48 100644
--- a/REUSE.toml
+++ b/REUSE.toml
@@ -2,6 +2,7 @@ version=1
 
 [[annotations]]
 path = [
+    ".ai/**",
     ".github/**",
     "*.md",
     "*.toml",
diff --git a/containers/repronim-reprostim/generate_container.sh b/containers/repronim-reprostim/generate_container.sh
index 003c9cf7..00dff281 100755
--- a/containers/repronim-reprostim/generate_container.sh
+++ b/containers/repronim-reprostim/generate_container.sh
@@ -5,65 +5,43 @@ set -eu
 
 thisdir=$(dirname "$0")
 
-PYTHON_VERSION=3.10
+MODE=${1:-default}
 
+PYTHON_VERSION=3.10
 PSYCHOPY_VERSION=2025.2.0
-PSYCHOPY_INSTALL_DIR=/opt/psychopy
-PSYCHOPY_VENV_NAME=psychopy_${PSYCHOPY_VERSION}_py${PYTHON_VERSION}
-PSYCHOPY_HOME=${PSYCHOPY_INSTALL_DIR}/${PSYCHOPY_VENV_NAME}
-PSYCHOPY_VENV_BIN=${PSYCHOPY_HOME}/.venv/bin
-
 REPROSTIM_VERSION=$(git describe --tags --abbrev=0 2>/dev/null || echo "0.0.1")
 # Decided to go without version to make diff easier to analyze etc
 REPROSTIM_SUFFIX=repronim-reprostim # -${REPROSTIM_VERSION}
-REPROSTIM_GIT_HOME=$(git rev-parse --show-toplevel)
 REPROSTIM_HOME=/opt/reprostim
+REPROSTIM_GIT_HOME=$(git rev-parse --show-toplevel)
 REPROSTIM_CAPTURE_ENABLED="${REPROSTIM_CAPTURE_ENABLED:-0}"
 REPROSTIM_CAPTURE_PACKAGES_DEV=""
-REPROSTIM_CAPTURE_PACKAGES_RUNTIME=""
-REPROSTIM_CAPTURE_BUILD="echo 'ReproStim capture build is disabled'"
-REPROSTIM_CAPTURE_CLEAN="echo 'ReproStim capture clean is disabled'"
+REPROSTIM_CAPTURE_PACKAGES_RUNTIME="mc"
 
+# include capture packages if enabled, two subsets: dev and runtime
+# dev packages are needed only during build time
+# runtime packages are needed during runtime and build time
 if [[ "$REPROSTIM_CAPTURE_ENABLED" == "1" ]]; then
   REPROSTIM_CAPTURE_PACKAGES_DEV="libyaml-cpp-dev libspdlog-dev catch2 libv4l-dev libudev-dev libopencv-dev libcurl4-openssl-dev nlohmann-json3-dev cmake g++"
-  REPROSTIM_CAPTURE_PACKAGES_RUNTIME="libyaml-cpp0.7 libfmt9"
-  REPROSTIM_CAPTURE_BUILD="cd \"$REPROSTIM_HOME/src/reprostim-capture\"; mkdir build; cd build; cmake ..; make; cd ..; cmake --install build; rm -rf \"$REPROSTIM_HOME/src/reprostim-capture/build\"; reprostim-videocapture -V"
-  REPROSTIM_CAPTURE_CLEAN="apt-get remove --purge -y $REPROSTIM_CAPTURE_PACKAGES_DEV && apt-get autoremove -y"
-  # Extend with packages hold if runtime packages env exist
-  if [[ -n "$REPROSTIM_CAPTURE_PACKAGES_RUNTIME" ]]; then
-      REPROSTIM_CAPTURE_CLEAN="apt-mark manual $REPROSTIM_CAPTURE_PACKAGES_RUNTIME && apt-mark hold $REPROSTIM_CAPTURE_PACKAGES_RUNTIME && $REPROSTIM_CAPTURE_CLEAN"
-  fi
-fi
-
-
-MODE=${1:-default}
-
-
-if [[ "$MODE" == "ci" ]]; then
-  echo "Running in CI/CD mode, install reprostim from current worktree"
-  REPROSTIM_COPY="${REPROSTIM_GIT_HOME} ${REPROSTIM_HOME}"
-  REPROSTIM_RUN_INSTALL="${PSYCHOPY_VENV_BIN}/pip install ${REPROSTIM_HOME}[all,disp_mon]"
-else
-  echo "Running in default mode, install reprostim from PyPI"
-  REPROSTIM_COPY=""
-  REPROSTIM_RUN_INSTALL="${PSYCHOPY_VENV_BIN}/pip install reprostim[all,disp_mon]==${REPROSTIM_VERSION}"
+  REPROSTIM_CAPTURE_PACKAGES_RUNTIME="mc libyaml-cpp0.7 libfmt9"
 fi
 
-
-
 generate() {
-  if [[ "$1" == docker && "$MODE" == "ci" ]]; then
-    REPROSTIM_COPY="reprostim ${REPROSTIM_HOME}"
+  # Somehow --copy source differs between docker and singularity
+  REPROSTIM_COPY_SRC="${REPROSTIM_GIT_HOME}"
+  if [[ "$1" == docker ]]; then
+    REPROSTIM_COPY_SRC="reprostim"
   fi
 
-  if [[ "$1" == singularity && "$MODE" == "ci" ]]; then
-    REPROSTIM_COPY="${REPROSTIM_GIT_HOME} ${REPROSTIM_HOME}"
-  fi
+  # copy the setup script to /opt/setup_container.sh
+  REPROSTIM_COPY_ARGS=( "--copy" "${REPROSTIM_COPY_SRC}/containers/repronim-reprostim/setup_container.sh" "/opt/setup_container.sh" )
 
-  if [[ -n "${REPROSTIM_COPY:-}" ]]; then
-    REPROSTIM_COPY_ARG="--copy ${REPROSTIM_COPY}"
-  else
-    REPROSTIM_COPY_ARG=""
+  # optionally copy the current worktree into the container
+  # for CI mode to build reprostim package from current code
+  # rather than from PyPI
+  if [[ "$MODE" == "ci" ]]; then
+    # add another --copy pair for CI
+    REPROSTIM_COPY_ARGS+=( "--copy" "${REPROSTIM_COPY_SRC}" "${REPROSTIM_HOME}" )
   fi
 
   # shellcheck disable=SC2034
@@ -87,15 +65,9 @@ generate() {
           vim wget strace time ncdu gnupg curl procps pigz less tree python3 python3-pip \
           "${REPROSTIM_CAPTURE_PACKAGES_RUNTIME}" \
           "${REPROSTIM_CAPTURE_PACKAGES_DEV}" \
-    --run "git clone https://github.com/wieluk/psychopy_linux_installer/ /opt/psychopy-installer; cd /opt/psychopy-installer; git checkout tags/v2.2.3" \
-    --run "/opt/psychopy-installer/psychopy_linux_installer --install-dir=${PSYCHOPY_INSTALL_DIR} --venv-name=${PSYCHOPY_VENV_NAME} --psychopy-version=${PSYCHOPY_VERSION} --additional-packages=psychopy_bids==2025.1.2,psychopy-mri-emulator==0.0.2 --python-version=${PYTHON_VERSION} --wxpython-version=4.2.3 -v -f" \
-    ${REPROSTIM_COPY_ARG} \
-    --run "${REPROSTIM_RUN_INSTALL}" \
-    --run "bash -c 'ln -s ${PSYCHOPY_HOME}/start_psychopy /usr/local/bin/psychopy'" \
-    --run "bash -c 'b=\$(ls ${PSYCHOPY_VENV_BIN}/python3); echo -e \"#!/bin/sh\n\$b \\\"\\\$@\\\"\" >| /usr/local/bin/python3; chmod a+x /usr/local/bin/python3'" \
-    --entrypoint python3 \
-    --run "bash -c '$REPROSTIM_CAPTURE_BUILD'" \
-    --run "bash -c '$REPROSTIM_CAPTURE_CLEAN'"
+    "${REPROSTIM_COPY_ARGS[@]}" \
+    --run "bash -c 'chmod a+rX /opt/setup_container.sh && PYTHON_VERSION=\"${PYTHON_VERSION}\" PSYCHOPY_VERSION=\"${PSYCHOPY_VERSION}\" REPROSTIM_VERSION=\"${REPROSTIM_VERSION}\" REPROSTIM_HOME=\"${REPROSTIM_HOME}\" REPROSTIM_GIT_HOME=\"${REPROSTIM_GIT_HOME}\" MODE=\"${MODE}\" REPROSTIM_CAPTURE_ENABLED=\"${REPROSTIM_CAPTURE_ENABLED}\" REPROSTIM_CAPTURE_PACKAGES_DEV=\"${REPROSTIM_CAPTURE_PACKAGES_DEV}\" REPROSTIM_CAPTURE_PACKAGES_RUNTIME=\"${REPROSTIM_CAPTURE_PACKAGES_RUNTIME}\" /opt/setup_container.sh'" \
+    --entrypoint python3
 #    --user=reproin \
 }
 
diff --git a/containers/repronim-reprostim/run_reprostim_ci.sh b/containers/repronim-reprostim/run_reprostim_ci.sh
index 44d2d406..e1ac01c4 100755
--- a/containers/repronim-reprostim/run_reprostim_ci.sh
+++ b/containers/repronim-reprostim/run_reprostim_ci.sh
@@ -26,10 +26,11 @@ elif [[ "$REPROSTIM_CONTAINER_TYPE" == "singularity" ]]; then
   REPROSTIM_CONTAINER_IMAGE="${REPROSTIM_CONTAINER_IMAGE:-./repronim-reprostim-${REPROSTIM_VERSION}.sing}"
 fi
 
-# Calculate entry point
+# Calculate entry point and command to run inside container
 REPROSTIM_CONTAINER_ENTRYPOINT=""
-if [ "$REPROSTIM_CONTAINER_RUN_MODE" = "reprostim-videocapture" ]; then
-    REPROSTIM_CONTAINER_APP="reprostim-videocapture"
+if [ "$REPROSTIM_CONTAINER_RUN_MODE" = "reprostim-videocapture" ] || [ "$REPROSTIM_CONTAINER_RUN_MODE" = "psychopy" ]; then
+    REPROSTIM_CONTAINER_APP="$REPROSTIM_CONTAINER_RUN_MODE"
+    # clear/remove python entrypoint for standalone apps
     if [ "$REPROSTIM_CONTAINER_TYPE" = "docker" ]; then
         REPROSTIM_CONTAINER_ENTRYPOINT="--entrypoint="
     fi
@@ -54,6 +55,19 @@ log "  [IMAGE]          : ${REPROSTIM_CONTAINER_IMAGE}"
 log "  [OVERLAY]        : ${REPROSTIM_OVERLAY}"
 log "  [ARGS]           : $*"
 
+#
+# Prepare XAUTHORITY path (fallback to $HOME/.Xauthority)
+# also before running docker container with psychopy UI allow
+# access to X server with:
+#
+#  xhost +local:root
+#    or
+#  xhost +local:docker
+#
+# and optionally to quiet Podman (when "Emulate Docker CLI" listed in logs):
+#  sudo touch /etc/containers/nodocker
+#
+XAUTHORITY_HOST="${XAUTHORITY:-$HOME/.Xauthority}"
 
 if [[ "$REPROSTIM_CONTAINER_TYPE" == "docker" ]]; then
   docker run --rm -i ${DOCKER_TTY} \
@@ -61,6 +75,8 @@ if [[ "$REPROSTIM_CONTAINER_TYPE" == "docker" ]]; then
     -v "${REPROSTIM_PATH}:${REPROSTIM_PATH}" \
     -w "${REPROSTIM_PATH}" \
     --env DISPLAY=$DISPLAY \
+    -v "${XAUTHORITY_HOST}:${XAUTHORITY_HOST}:ro" \
+    -v /tmp/.X11-unix:/tmp/.X11-unix \
     ${REPROSTIM_OVERLAY} ${REPROSTIM_CONTAINER_IMAGE} \
     ${REPROSTIM_CONTAINER_APP} "$@"
 elif [[ "$REPROSTIM_CONTAINER_TYPE" == "singularity" ]]; then
diff --git a/containers/repronim-reprostim/setup_container.sh b/containers/repronim-reprostim/setup_container.sh
new file mode 100755
index 00000000..3c16dd8f
--- /dev/null
+++ b/containers/repronim-reprostim/setup_container.sh
@@ -0,0 +1,121 @@
+#!/bin/bash
+# shellcheck disable=SC2086,SC2034
+
+# This is internal script used by Docker/Singularity to setup the container
+# and it's automatically copied into the container image under /opt/setup_container.sh
+# location. It is not meant to be run directly by users.
+#
+# Note: env variables passed explicitly from generate_container.sh script:
+#   $MODE
+#   $PYTHON_VERSION
+#   $PSYCHOPY_VERSION
+#   $REPROSTIM_VERSION
+#   $REPROSTIM_HOME
+#   $REPROSTIM_GIT_HOME
+#   $REPROSTIM_CAPTURE_ENABLED
+#   $REPROSTIM_CAPTURE_PACKAGES_DEV
+#   $REPROSTIM_CAPTURE_PACKAGES_RUNTIME
+
+set -eu
+
+thisdir=$(dirname "$0")
+
+PSYCHOPY_INSTALL_DIR=/opt/psychopy
+PSYCHOPY_VENV_NAME=psychopy_${PSYCHOPY_VERSION}_py${PYTHON_VERSION}
+PSYCHOPY_HOME=${PSYCHOPY_INSTALL_DIR}/${PSYCHOPY_VENV_NAME}
+PSYCHOPY_VENV_BIN=${PSYCHOPY_HOME}/.venv/bin
+
+
+# Install psychopy_linux_installer from GitHub
+echo "Install psychopy_linux_installer from GitHub..."
+git clone --branch v2.2.4 --depth 1 https://github.com/wieluk/psychopy_linux_installer/ /opt/psychopy-installer
+cd /opt/psychopy-installer
+
+# Install PsychoPy via psychopy_linux_installer
+echo "Install PsychoPy v${PSYCHOPY_VERSION} via psychopy_linux_installer..."
+/opt/psychopy-installer/psychopy_linux_installer --install-dir=${PSYCHOPY_INSTALL_DIR} --venv-name=${PSYCHOPY_VENV_NAME} --psychopy-version=${PSYCHOPY_VERSION} --additional-packages=psychopy_bids==2025.1.2,psychopy-mri-emulator==0.0.2 --python-version=${PYTHON_VERSION} --wxpython-version=4.2.3 --cleanup -v -f
+# Create symlink to psychopy executable
+ln -sf "${PSYCHOPY_HOME}/start_psychopy" /usr/local/bin/psychopy
+
+# Install reprostim package from PyPI or from current worktree in CI mode
+if [[ "$MODE" == "ci" ]]; then
+  echo "Running in CI/CD mode, install reprostim from current worktree"
+  "${PSYCHOPY_VENV_BIN}/pip" install "${REPROSTIM_HOME}[all,disp_mon]"
+else
+  echo "Running in default mode, install reprostim from PyPI"
+  "${PSYCHOPY_VENV_BIN}/pip" install "reprostim[all,disp_mon]==${REPROSTIM_VERSION}"
+fi
+
+# Create symlink to python3 in psychopy venv as default python3
+echo "Creating symlink to python3 in psychopy venv as default python3"
+b=$(ls "${PSYCHOPY_VENV_BIN}/python3")
+echo -e "#!/bin/sh\n$b \"\$@\"" >| /usr/local/bin/python3
+chmod a+x /usr/local/bin/python3
+
+if [[ "$REPROSTIM_CAPTURE_ENABLED" == "1" ]]; then
+  # Build reprostim-capture from source
+  echo "Building reprostim-capture from source..."
+  cd "${REPROSTIM_HOME}/src/reprostim-capture"
+  mkdir build
+  cd build
+  cmake ..
+  make
+  cd ..
+
+  # Install the built binary
+  echo "Installing reprostim-capture..."
+  cmake --install build
+
+  # Clean build files
+  rm -rf "${REPROSTIM_HOME}/src/reprostim-capture/build"
+
+  # Verify installation
+  echo "Verifying reprostim-capture installation..."
+  reprostim-videocapture -V
+
+  # Cleanup reprostim-capture packages
+  #
+  # Keep runtime packages marked as manual to avoid their removal
+  if [[ -n "$REPROSTIM_CAPTURE_PACKAGES_RUNTIME" ]]; then
+    echo "Marking reprostim-capture runtime packages as manual to avoid their removal: ${REPROSTIM_CAPTURE_PACKAGES_RUNTIME}"
+    apt-mark manual $REPROSTIM_CAPTURE_PACKAGES_RUNTIME
+    apt-mark hold $REPROSTIM_CAPTURE_PACKAGES_RUNTIME
+  fi
+
+  # Remove dev packages
+  echo "Removing reprostim-capture development packages: ${REPROSTIM_CAPTURE_PACKAGES_DEV}"
+  apt-get remove --purge -y ${REPROSTIM_CAPTURE_PACKAGES_DEV}
+  apt-get autoremove -y
+fi
+
+# Remove psychopy-installer
+echo "Removing psychopy-installer..."
+rm -rf /opt/psychopy-installer
+
+# Remove unnecessary dirs/files from the copied worktree
+echo "Cleaning up copied reprostim worktree..."
+rm -rf "${REPROSTIM_HOME}/.ai"
+rm -rf "${REPROSTIM_HOME}/.git"
+rm -rf "${REPROSTIM_HOME}/.github"
+rm -rf "${REPROSTIM_HOME}/.idea"
+rm -rf "${REPROSTIM_HOME}/.pytest_cache"
+rm -rf "${REPROSTIM_HOME}/Events"
+rm -rf "${REPROSTIM_HOME}/Parsing"
+rm -rf "${REPROSTIM_HOME}/QRCoding"
+rm -rf "${REPROSTIM_HOME}/dist"
+rm -rf "${REPROSTIM_HOME}/docs"
+rm -rf "${REPROSTIM_HOME}/examples/exp-alpha"
+rm -rf "${REPROSTIM_HOME}/temp"
+rm -rf "${REPROSTIM_HOME}/venv"
+rm -rf "${REPROSTIM_HOME}/.gitignore"
+
+# Configure permissions
+echo "Configuring permissions to allow non-root users to run PsychoPy and ReproStim..."
+if [[ -d /opt ]]; then
+  chmod a+rX -R /opt || true
+fi
+if [[ -d /root/.psychopy3 ]]; then
+  chmod a+rX -R /root/.psychopy3 || true
+fi
+
+echo "Container setup completed: Python v${PYTHON_VERSION} + PsychoPy v${PSYCHOPY_VERSION} + ReproStim v${REPROSTIM_VERSION}"