Polychromatic polarization microscopy is a real-time collagen imaging method in clinical histopathology compatible with brighfield microscopy.
| Brightfield | PPM |
|---|---|
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Install anaconda/miniconda (https://www.anaconda.com/distribution/) and activate conda base in terminal.
Create the environment.
$ conda env create --name ppm --file env.yml
$ conda activate ppm
$ pip install pycromanager
Jupyter notebook is recommended
$ conda install -c conda-forge jupyterlab
- Put positive images and negative images in "data-sample/+5" and "data-sample/-5" folders, respectively.
- Put brightfield images in "data-sample/bf" (optional).
The positive images, negative images, and brightfield images need to have the same name for each sample. - Put background images in "data-sample/bg", named "b-5.tif" and "b+5.tif" (optional). These two images are for white-balance correction. The images will be corrected based on estimated values if no background images are provided.
Open ppm-process.ipynb and execute the cells, or run .py in terminal
python ppm-process.py
Select the "data-sample" folder in the pop-up window.
Check outputs in "data-sample/results" folder.
If you use Jupyter Notebook, the results images will also be printed in the notebook.