Modeling of local structure with a dictionary of image patches
- applied to the study of Lung ECM proteins
To reproduce the results from our paper (link to come), you will need to clone this repository or download it as a .zip file. Then, download the input_data and results_justDictionaries folders from DTU Data at XX. Place both within the Lung_ECM folder, besides the code folder. Rename 'results_justDictionaries' to 'results' so as to reproduce the exact results from our paper. Under the same DTU Data link you will also find the complete set of results under 'results_complete'.
The following figure is a schematic view of the code, results and input_data folders. The table below describes further the content of the code folder found in this repository.
Code contains:
| File name | Description | Input | Output |
|---|---|---|---|
| lung_lif_to_png.py | Transforms Leica microscope format into a png | .lif file pr. sample | input_data/raw |
| microscopy_analysis.py | Helper functions | ||
| image_preprocessing.py | Equalises contrast across images and channels, and computes max. projections | input_data/raw | input_data/maximum_projections and postprocessed_maxProjs |
nogenerate data_corrected_bis, where each 3D scan is stored as a sequence of .png files under a folder with 'frame' as prefix.