mibilib

Python client for IONpath MIBItracker API, plus utility functions for working with MIBItiff images.

https://ionpath.github.io/mibilib/

Setup

Install Python 3.7

Install the Python 3.7 version of Miniconda. Even if your system already has a version of Python installed, it is strongly recommended to use the conda environment manager to install and manage this library's dependencies.

Option A (Development): Clone repository and create environment

This option downloads the source code and creates a development environment. It does not add this library to the path, so if your use case is to import it into other projects rather than interact with the source, Option B is recommended.

cd <path/to/where/you/want/to/install/project>
git clone https://github.com/ionpath/mibilib
cd mibilib

conda env create -f environment.yml
conda activate mibilib

Option B (Usage): Install with pip

This option is useful if you want this library to be installed as part of an existing environment or as a dependency inside a requirements.txt file. You may install a particular release using its tag (recommended)

pip install git+git://github.com/ionpath/mibilib@v1.2.8

or a branch (that may be under development with frequent changes)

pip install git+git://github.com/ionpath/master

Usage

To use the MIBItracker API, you will need to use the backend url listed in the About page. This can be accessed after you have logged in from the menu under your username in the upper right of the window.

from mibitracker.request_helpers import MibiRequests

request = MibiRequests(
    'https://your-mibitracker-backend.appspot.com',
    'user@example.com',
    'password1234'
)
image_id = request.image_id('20180927', 'Point3')
image_details = request.get('/images/{}/'.format(image_id))

More examples can be found in the following notebooks:

• MIBItracker_API_Tutorial

• MibiImage_Tutorial

• SingleCellSpatialExamples

Full documentation for this library can be found at https://ionpath.github.io/mibilib/.

Sample data

Access to sample data to run the tutorials in the notebooks can be requested by creating an account at the following URL: https://mibi-share.ionpath.com.