### 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'.
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@@ -8,7 +9,10 @@ Code contains:
| File name | Description | Input | Output |
| --------- | ----------- | ----- | ------ |
| lung_to_lif.py | Used to transform data acquired with a Leica microscope into a format we can work with | EDIT | input_data/raw |
| 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.
