-
This software package can be utilized in fluorescence imaging analysis to effectively communicate information present within video files. Functions present within the program are designed to:
- Identify Regions of Interest (R.O.I.) based on relative pixel brightness
- Accumulate ROI counts throughout the stack and return a frequency heat map
- Accumulate ROI intensity throughout the stack and return an intensity heat map
|- README.md
|- flashing_lights/
|- __init__.py
|- GenerateHeatMap.py
|- GenerateIntensitymap.py
|- ROILocator.py
|- tests/
|- __init__.py
|- test_GenerateHeatMap.py
|- test_GenerateIntensityMap.py
|- test_ROILocator.
|- __pycache__/
|- data/
|- July_test.tif
|- test_ROI.tif
|- test_gray.tif
|- __pycache__/
|- doc/
|- README.md
|- functionality.md
|- usage_cases.md
|- presentations/ (tech_review and final presentation slides)
|- module_structures/ (images of project module structures)
|- examples/
|- README.md
|- GenerateHeatMap.example.ipynb
|- GenerateIntensityMap.example.ipynb
|- ROILocator.example.ipynb
|- ExampleFrequencyHeatmapImages/
|- ExampleIntensityHeatmapImages/
|- ExampleROILocatorVideos/
|- setup.py
|- .travis.yml
|- environment.yml
|- .pylintrc (for pylint conflict with opencv)
|- .gitignore
|- lights.gif (Star Trek Video)
|- ROI_video_example.gif
|- LICENSE
- Included within the root of the repository is a virtual environment
pre-suited to run
flashing_lights- The virtual environment is located within environment.yml
- To create the virtual environment from the .yml file:
conda env create -f environment.yml - To activate the virtual environment:
conda activate flashing_lights_env - The environment contains:
- Python 3.8 from miniconda3
- numpy
- os
- pandas
- matplotlib
- skimage
- cv2
- Before using, please download some sample data that you can test the package with (UW members only):
- https://drive.google.com/open?id=1_QdBC2IoNTqGhwI5b9mVSK-13hiPy7nv (Belongs to Chris)
- https://drive.google.com/open?id=1mJFNPfbdzfQ6NuFcVwRL8FVMmbw3L43K (Belongs to Chris)
- https://drive.google.com/open?id=1ZkAAcj-qXpCypLGnU8HuU47QkjAKdvko (Belongs to July)
- https://drive.google.com/open?id=12Noa3-JsaPup9Ao9WEqEOqzdbKAMogCA (Belongs to July)
- flashing_lights can be executed through a jupyter notebook.
- It is recommended to run the code within the included virtual environment to avoid dependency hell
- We have included filled examples of jupyter notebooks
within
flashing_lights/examples/workedthat demonstrate how to use the code. To access these notebooks, enter the following into the command line:jupyter notebook flashing_lights/examples/worked/<notebook name>
- In regards to PEP8 compliance of the GenerateHeatMap.py file, pylint shoots back an error I1101. The '.pylintrc' file can be downloaded to prevent those from showing up in the terminal.
- A big shout to Professor Dave Beck, Professor Ting Cao, Caityln Wolf, Jimin Qian, Ted Cohen, and Torin Stetina for all of their help during the development of this package.
- Thank you to Professor Zhang & Professor Nance's labs for providing the videos that we could analyze.