Skip to content
Snippets Groups Projects
Select Git revision
  • master
1 result

Lung-ECM

  • Open with
  • Download source code
  • Your workspaces

      A workspace is a virtual sandbox environment for your code in GitLab.

      No agents available to create workspaces. Please consult Workspaces documentation for troubleshooting.

  • monj's avatar
    monj authored
    06102015
    History
    Name Last commit Last update
    code
    .gitignore
    README.md

    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 https://doi.org/10.11583/DTU.16652065. Place both within the Lung_ECM folder, besides the code folder. Rename results_justDictionaries to results if you want 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 content in the results and input_data folders (at DTU Data) and the code in this repository. The table below describes further the content of the code folder found in this repository.

    TO DO: ADD schematic

    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
    lung_feature_patch_allPatients_singleProtein.py Single-protein analysis postprocessed max. projs. results/..._single
    lung_feature_patch_allPatients_twoProtein.py Two-protein analysis postprocessed max. projs. results/..._dropout
    lung_feature_patch_allPatients_threeProtein.py Three-protein analysis postprocessed max. projs. results/..._triple

    Code developed by Monica J. Emerson monj@dtu.dk with contributions from Anders B. Dahl abda@dtu.dk.