/colon_organoid_bf

Analysis of brighfield images of colonoids growing in Matrigel droplets to extract morphological features and object counts.

Primary LanguageJupyter NotebookBSD 3-Clause "New" or "Revised" LicenseBSD-3-Clause

colon_organoid_bf

Analysis of brighfield images of colonoids growing in Matrigel droplets to extract morphological features and object counts.

Instructions

  1. In order to run these Jupyter notebooks and .py scripts you will need to familiarize yourself with the use of Python virtual environments using Mamba. See instructions here.

  2. Then you will need to create a virtual environment either using the following command or recreate the environment from the .yml file you can find in the envs folder:

    mamba create -n napari-devbio python=3.9 devbio-napari plotly pyqt -c conda-forge

  3. Create a data folder in the root directory. Place all of your folders inside the ./data/ directory.

  4. Activate your venv and launch a JupyterLab server by typing this in your command line prompt:

    mamba activate napari-devbio

    jupyter lab

  5. Open 1_image_analysis.ipynb and run all cells.