Working in collaboration with cancer research UK to automate the acquisition & analysis of images used to monitor stem cell growth

To set up your virtual environment and install the relevant packages

• Run the command source setup_linux.sh, for Linux based systems
• Run the command setup_windows.bat, for Windows based systems

• On Linux run the command source bin/activate
• deactivate will deactivate virtualenv environment

• Run the project using python AutoDAC.py

• Generate HTML test coverage

  • pytest --cov=ImageProcessing/src --cov=MicroscopeInterface/src --cov-report term --cov-report html ImageProcessing/tests MicroscopeInterface/tests

• Run tests

  • pytest --cov=ImageProcessing/src --cov=MicroscopeInterface/src --cov-report term ImageProcessing/tests MicroscopeInterface/tests

One can run python3 -m http.server inside the htmlcov directory, this will launch a http server which you can access via the browser at localhost:8000 (usually)

The project is split into two major components: Microscope Interface and Image Analysis

• Responsible for handling the interaction with the microscope
• Clicks buttons on LASAF software
• Extracts cells from microsocope images for analysis

• Responsible for analysing extracted images
• Segments images of cells
• Scores segmented image of cell

• The source files have been annotated with comments describing the purpose of the functions within them. These can be read directly from the source files or by running pydoc <path-to-file> from the root level directory
• Documentation for each of the files can also be viewed as a webpage. For example, running pydoc -w MicroscopeInterface/src/LeicaUI.py from the root level directory will generate a LeicaUI.html file for the LeicaUI.py program file. The html file can be double clicked on to open, or can be opened via open LeicaUI.html on the terminal.

• Zubair Chowdhury
• Sarah Baka
• Harry Uglow
• Ioannis Gabrielides
• Andy Hume