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Lung-ECM

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    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.