mibi-bin-tools

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Toolbox for extracting tiff images from MIBIScope .bin files.

We suggest using toffy for more in depth .bin file extraction which also provides more diagnostic tools and post-extraction processing steps.

Installation:

You can install the package in your own Python environment, or if you'd like we have a Conda environment set up to use.

conda env create -f environment.yml

PyPI

pip install mibi-bin-tools

Source

Open terminal and navigate to where you want the code stored.

Then input the command:

git clone https://github.com/angelolab/mibi-bin-tools.git
cd mibi-bin-tools
pip install .

Development

This project is in early development and we make may make breaking changes and improvements. If you want to update the version on your computer to have the latest changes, perform the following steps.

First pull to get the latest version of mibi-bin-tools. Then install the package in editable mode with your python environment of choice activated.

git pull
pip install -e .

To run the tests

pytest

Questions?

If that doesn't answer your question, you can open an issue. Before opening, please double-check and see that someone else hasn't opened an issue for your question already.