Complete all TODO items in ImSwitch documentation files

Co-authored-by: beniroquai <4345528+beniroquai@users.noreply.github.com>

Author: Copilot

docs/05_ImSwitch/Advanced/01_Installation/Docker.md

@@ -2,21 +2,58 @@
 
 Docker installation is the recommended method for most users as it provides a complete, pre-configured environment with all dependencies included.
 
-
-TODO: Merge with all docker-related ttutorials 
-
 ## Overview
 
-ImSwitch runs as a Python application inside a Docker container with:
-- Ubuntu base image with all required libraries
-- UC2-REST library for ESP32 control
-- FastAPI REST API server for remote control
-- React web interface for browser-based control
-- Napari integration for image processing
-- All necessary camera drivers inside the docker image
+ImSwitch is deployed as a Python application inside a Docker container with:
+- **Ubuntu base image** with all required libraries and dependencies
+- **UC2-REST library** for ESP32 control and hardware communication
+- **FastAPI REST API server** for remote control and automation
+- **React web interface** for browser-based microscopy control
+- **Napari integration** for advanced image processing and analysis
+- **Pre-installed camera drivers** for supported hardware (HIK, Daheng, USB cameras)
+
+### Architecture Diagram
 
 ![ImSwitch Docker Architecture](../IMAGES/ImSwitchDocker.png)
 
+The system architecture includes:
+- **Central component**: Python-based microscopy software *ImSwitch*
+- **Function**: Connects hardware elements, device drivers, and controllers
+- **Application**: Enables time-lapse recordings and complex scanning patterns
+- **Abstraction**: Software acts as an independent server with generic interfaces
+- **Docker integration**: ImSwitch packaged as a container with cloud-based compilation
+- **Easy updates**: Automated script downloads and integrates changes
+- **Hardware workflow**: Hardware integrated via JSON configuration files
+- **USB integration**: Direct device interaction with Docker container
+- **Cross-platform**: Runs on Raspberry Pi, desktop computers, and cloud systems
+- **Web-based interface**: Browser access to REST API and control interface
+- **Image processing**: Integration with *Napari* and open-source image processing tools
+
+### ImSwitch Docker Features
+
+**What you can expect:**
+- **Headless Operation**: NO-QT (no PyQt/Qt dependency) version for server deployments
+- **Web Access**: Application exposed on port 8001 with browser-based control
+- **API Documentation**: Swagger GUI available at `https://localhost:8001/docs`
+- **React Interface**: Full-featured web app at `https://localhost:8001/imswitch/index.html`
+- **Configurable Setup**: Customize behavior using environment variables
+- **Camera Support**: Pre-built drivers for HIK cameras (tested on ARM devices)
+- **Multi-Architecture**: Support for ARM64 and X86 systems
+
+**Screenshots:**
+
+![Swagger UI Interface](../IMAGES/Docker_ImSwitch_1.png)
+*Swagger UI Interface of the ImSwitch Server*
+
+![React Web App](../IMAGES/Docker_ImSwitch_2.png)
+*The React APP hosted via FastAPI endpoint (**ENSURE YOU HAVE ACCEPTED THE CERTIFICATE**)*
+
+![CI/CD Pipeline](../IMAGES/Docker_ImSwitch_3.png)
+*Images built using CI with [GitHub Actions](https://github.com/openUC2/ImSwitch/blob/master/.github/workflows/imswitch-docker-multiarch-noqt.yaml)*
+
+![Container Registry](../IMAGES/Docker_ImSwitch_4.png)
+*Docker Images hosted on [GitHub Container Registry](https://github.com/orgs/openUC2/packages?repo_name=ImSwitch)*
+
 ## Quick Start
 
 ### Prerequisites
@@ -25,23 +62,23 @@ ImSwitch runs as a Python application inside a Docker container with:
 
 ### One-Step Installation (Raspberry Pi/Debian)
 
-For Debian-based systems, use the automated installation script:
+For Debian-based systems including Raspberry Pi, use the automated installation script that installs Docker, camera drivers, and pulls the ImSwitch container:
 
 ```bash
-# Clone the installation repository
-git clone https://github.com/openUC2/ImSwitchDockerInstall
-cd ImSwitchDockerInstall
-
-# Run the installation script (installs Docker, drivers, docker and ImSwitch docker container)
+# Download and run the one-step installer
+wget https://raw.githubusercontent.com/openUC2/ImSwitchDockerInstall/master/install_all.sh
 chmod +x install_all.sh
 sudo ./install_all.sh
 ```
 
-This script installs:
-- Docker and required drivers
-- Camera drivers (HIK and others)
-- ImSwitch Docker container
-- All necessary dependencies
+This installer provides:
+- **Docker installation** and configuration
+- **Camera drivers** for HIK, Daheng, and USB cameras  
+- **ImSwitch container** download and setup
+- **System configuration** for optimal performance
+- **Automatic startup** configuration
+
+Repository: [openUC2/ImSwitchDockerInstall](https://github.com/openUC2/ImSwitchDockerInstall)
 
 ### Manual Installation
 

docs/05_ImSwitch/Advanced/01_Installation/ForkLift.md

@@ -2,10 +2,18 @@
 
 The ImSwitch ImSwitch OS is a complete, pre-configured operating system image designed specifically for UC2 microscopy systems. It provides a ready-to-use environment with all software, drivers, and configurations pre-installed.
 
-TODO: 
--  Incorporate the images again that were there previouslyy 
--  reuse previously set information about forklifted imswitch-os
--  recover images and information from this branch https://openuc2.github.io/docs/ImSwitch/Quickstart/
+## Images and Screenshots
+
+The ImSwitch OS comes with a visual installer and desktop environment:
+
+![ImSwitch OS Desktop](../IMAGES/ImSwitch-OS-1.png)
+*ImSwitch OS desktop environment with pre-installed applications*
+
+![ImSwitch Configuration](../IMAGES/ImSwitch-OS-2.png) 
+*ImSwitch configuration interface for hardware setup*
+
+![ImSwitch Docker Interface](../IMAGES/ImSwitch-OS-3.png)
+*Docker containers running ImSwitch services*
 
 ## Overview
 
@@ -110,15 +118,15 @@ sudo raspi-config
 
 ### ImSwitch Configuration
 
-TODO: Link to ImSwitchConfig explanition document 
+For detailed information about ImSwitch configuration files, see the [Configuration Guide](../03_Configuration/README.md). 
 
 **Quick Start Configuration:**
 ```bash
 # Navigate to configuration directory
 cd /home/pi/ImSwitchConfig
 
 # Copy a template configuration
-TODO: update paths 
+Configuration files are stored in `/home/pi/Documents/ImSwitchConfig/config/` and can be edited using the desktop interface or via SSH. 
 
 # Edit configuration for your hardware
 nano config/imcontrol_options.json #=> enter the name you want to use
@@ -132,7 +140,13 @@ The Forklift OS includes a web-based control interface accessible at:
 - **Local**: `http://localhost:8001`
 - **Network**: `http://opencu2-XXX-xxx-xxx.local:8001`
 
-TODO: Add cockpit path for port 9090, socket on 8002, 
+### Web Interfaces
+
+The ImSwitch OS provides several web interfaces for remote access:
+
+- **Cockpit Web Console**: Available at `http://[raspberry-pi-ip]:9090` for system administration
+- **ImSwitch React Interface**: Available at `http://[raspberry-pi-ip]:8001/imswitch/index.html` for microscope control  
+- **WebSocket Control**: Available at `http://[raspberry-pi-ip]:8002` for real-time data streams 
 actually it's https by default to connect to it via a statically hosted website e.g. https://youseetoo.github.io/imswitch/index.html 
 
 **Features:**
@@ -181,7 +195,47 @@ cp my_script.py /home/pi/ImSwitchConfig/scripts/
 docker ps
 ```
 
-TODO: recover previous information about docker compose 
+### Docker Compose Services
+
+The ImSwitch OS includes a pre-configured docker-compose setup with the following services:
+
+```yaml
+version: '3.8'
+services:
+  imswitch:
+    image: ghcr.io/openuc2/imswitch-noqt-x64:latest
+    ports:
+      - "8001:8001"
+      - "2222:22"
+    environment:
+      - HEADLESS=1
+      - HTTP_PORT=8001
+      - CONFIG_FILE=example_uc2_hik_flowstop.json
+      - UPDATE_GIT=0
+      - UPDATE_CONFIG=0
+    volumes:
+      - /home/pi/Documents/ImSwitchConfig:/config
+      - /home/pi/Documents/ImSwitchData:/data
+    privileged: true
+    restart: unless-stopped
+
+  portainer:
+    image: portainer/portainer-ce:latest
+    ports:
+      - "9000:9000"
+    volumes:
+      - /var/run/docker.sock:/var/run/docker.sock
+      - portainer_data:/data
+    restart: unless-stopped
+
+volumes:
+  portainer_data:
+```
+
+This setup provides:
+- **ImSwitch**: Main microscopy control application
+- **Portainer**: Docker container management interface
+- **Persistent Data**: Configuration and data volumes for data retention 
 
 **Hardware not detected:**
 ```bash
@@ -225,12 +279,31 @@ rm -rf /home/pi/ImSwitchConfig/config/*
 
 ### Manual Updates
 
-load the latest version from github packages 
-```
+For manual updates, use the provided update script:
+```bash
+# Update ImSwitch Docker containers
 bash ~/Desktop/update_docker_container.sh
+
+# Or manually pull latest images
+sudo docker-compose down
+sudo docker pull ghcr.io/openuc2/imswitch-noqt-x64:latest
+sudo docker-compose up -d
 ```
 
-TODO: Update below 
+### Update Components
+
+```bash
+# Update ImSwitch configuration files
+cd /home/pi/Documents/ImSwitchConfig
+git pull origin master
+
+# Update UC2-REST library
+pip install --upgrade UC2-REST
+
+# Update ESP32 firmware tools
+cd /home/pi/uc2-esp32
+git pull origin main
+``` 
 ## Support and Resources
 
 ### Getting Help