MAGS Organoid Analysis is the software developed for image analysis of 2d enteroid cultures [1]. This set of code accompanies a paper on 2d enteroid culture and analysis, which should be cited for this code [2].
The package was developed with Python. To install the correct version of Python and required packages, follow one of the two steps.
The easiest way to set up the appropriate environment is through conda. Miniconda3 can be installed at https://docs.conda.io/en/latest/miniconda.html
After installing Miniconda, download the package and navigate to the top organoid_analysis folder. Setup the Python environment with the following command.
conda env create --file=environment.yml
A conda environment named mags will be created. Activate the environment to run the scripts in this package. The environment can be activated with the following command
conda activate mags
The required Python version and packages can also be installed manually. The required version and packages are listed in environment.yml
FIJI is used to run one of the functions in pipeline. Install FIJI at https://imagej.net/Fiji/Downloads.
Java may be required to run FIJI in command line and can be downloaded here at http://jdk.java.net or https://adoptopenjdk.net
1: Thorne, C.A.*, Chen, I.W.*, Sanman, L.E., Cobb, M.H., Wu, L.F., and Altschuler, S.J. (2018). Enteroid Monolayers Reveal an Autonomous WNT and BMP Circuit Controlling Intestinal Epithelial Growth and Organization. Dev. Cell 44, 624–633.e4.
2: Sanman, L.E.*, Chen, I.W.*, Bieber, J.M.*, Steri, V., Trentesaux, C., Hann, B., Klein, O.D., Wu, L.F., and Altschuler, S.J. (2020). Transit-amplifying cells coordinate changes in intestinal epithelial cell type composition.