python lung morphometrics

A python module for performing morphometric measurements on microscopy images of lung tissue.

Status

Run it in a container

$ docker run -v ./data:/data docker.io/sylviamic/python_lung_morphometrics:latest do-mli /data/image_001.tif

Installation

$ git clone git://github.com/sylviamic/python_lung_morphometrics
$ cd python_lung_morphometrics
$ pip install -U .

CLI usage

Measure the mean linear intercept (MLI) of one image and print results to console:

$ python-lung-morphometrics do-mli image_001.tif

Measure the MLI of one image and save the test chords to a file in a specific directory:

$ python-lung-morphometrics do-mli --save-chords --save-dir ./my_output_dir image_001.tif

Measure the MLI of many images and save the results:

$ ls -1 ./image_*.tif | xargs -I {} python-lung-morphometrics do-mli {} > ./results.tsv

Measure the MLI of many images in parallel and save the results:

$ parallel -j5 --bar python-lung-morphometrics do-mli ::: ./image_*.tif > ./results.tsv``

Credits

This package was created by Sylvia N. Michki.

This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.

License

Free software: GNU General Public License v3