# Autonomous Laboratory Workflow Archive This archive contains the supporting code, design files, experimental data, images, and videos associated with the autonomous laboratory workflow developed for the PhD thesis. The material documents both the software and hardware infrastructure used to automate sample preparation, sample handling, imaging, and data collection for the algae optimisation workflow. The archive is divided into six main parts. Each part has its own README file with more specific information about folder contents, file types, and intended use. --- ## Archive contents | Archive | Description | |---|---| | `ACL_KMR2_ws-master.zip` | KUKA Sunrise Workbench workspace for the KMR iiwa mobile manipulator. | | `ARChemist Code.zip` | ARChemist/ROS code used to coordinate the autonomous laboratory workflow. | | `CAD & Schematics.zip` | CAD models, schematics, and drawings for custom hardware components. | | `Experimental Data.zip` | Main optimisation dataset, workflow recipes, configuration files, run logs, and supporting data. | | `Testing Images.zip` | Raw image datasets from imaging and colour-analysis development tests. | | `Video's.zip` | Demonstration videos of robotic handling, fume hood testing, and sample rack loading. | --- ## 1. KUKA robot workspace `ACL_KMR2_ws-master.zip` contains the KUKA Sunrise Workbench projects used with the KMR iiwa robotic platform. This includes Java-based robot applications, navigation-related tasks, gripper control, and station-specific handling routines. The files are intended to be imported into KUKA Sunrise Workbench and used with the relevant KUKA hardware, rather than run as a standalone software package. See: `README_ACL_KMR2_ws.md` --- ## 2. ARChemist workflow code `ARChemist Code.zip` contains the ARChemist-based software layer used to coordinate the autonomous workflow. It includes the ROS/catkin workspace, workflow manager code, station handlers, device drivers, recipe files, and configuration files. This code links the KUKA platform, Chemspeed FLEX, lightbox imaging station, and input/output stations into a single automated workflow. See: `README_ARChemist_Code.md` --- ## 3. CAD and schematics `CAD & Schematics.zip` contains design documentation for the custom hardware developed during the project. This includes CAD files for the six-well vial rack and schematic drawings for the growth chamber, lightbox, and large rack holder. These files are intended to document the physical system and support reconstruction, modification, or explanation of the hardware design. See: `README_CAD_and_Schematics.md` --- ## 4. Experimental data `Experimental Data.zip` contains the main data generated during the autonomous algae optimisation campaign. It includes the processed dataset, optimisation recipes, ARChemist configuration files, run logs, raw imaging outputs, and supporting testing data. The main spreadsheet records the sample formulations and corresponding image-derived response values used for optimisation. See: `README_Experimental_Data.md` --- ## 5. Testing images `Testing Images.zip` contains raw images collected during early imaging and colour-analysis development. These include bleach dilution tests, dye sample images, camera-location tests, and black-background imaging tests. The images support method development by documenting how sample appearance, background, lighting, and camera position influenced image capture. See: `README_Testing_Images.md` --- ## 6. Videos `Video's.zip` contains short demonstration videos from robotic and automation testing. These videos show examples of KUKA and Panda robot tests, fume hood interaction, and sample rack loading. They are intended as supporting visual material rather than quantitative experimental data. See: `README_Videos.md` --- ## How the archives relate to the thesis workflow Together, the six archives document the major layers of the autonomous system: 1. **Physical hardware** — growth chamber, lightbox, racks, rack holders, and robotic handling hardware. 2. **Robot control** — KUKA Sunrise applications for movement, gripping, navigation, and station interaction. 3. **Workflow orchestration** — ARChemist and ROS code for coordinating stations, recipes, and experimental execution. 4. **Experimental records** — optimisation data, recipe files, run logs, and images produced during testing and autonomous operation. 5. **Supporting visual evidence** — testing images and videos demonstrating the development and operation of the system. This structure is intended to make the archive usable both as thesis supporting material and as a reference for future researchers wishing to understand, reproduce, or adapt the workflow. --- ## Recommended reading order For a high-level understanding of the system, start with: 1. `README_Overall_Project_Archive.md` — this file. 2. `README_CAD_and_Schematics.md` — physical system overview. 3. `README_ARChemist_Code.md` — workflow control software. 4. `README_ACL_KMR2_ws.md` — KUKA robot control workspace. 5. `README_Experimental_Data.md` — main dataset and experimental records. 6. `README_Testing_Images.md` and `README_Videos.md` — supporting visual material. --- ## Safety and reproducibility notes The software and files in this archive relate to real laboratory automation hardware. They should not be used to operate robots, liquid-handling systems, or other laboratory equipment without appropriate training, safety checks, calibration, and institutional approval. Before attempting to reuse or adapt the system, users should verify: - robot frames, tool definitions, and station coordinates; - emergency stops, light curtains, and other safety interlocks; - Chemspeed method files and deck layouts; - recipe contents and reagent identities; - camera position, lighting, and image-analysis settings; - compatibility with the local software, hardware, and laboratory environment. The files are provided as a record of the system used during the PhD project and may require modification before use in any new installation. --- ## Notes on file naming Some archive names and folders preserve the original spelling and formatting used during the project, for example `Recipies` and `Video's.zip`. These names have been left unchanged to preserve the original project structure and avoid breaking file paths. macOS metadata files such as `.DS_Store` or `._*` may appear in some archives. These are not part of the experimental or design record and can be ignored.