This is 🍒 Griottes🍒 a tool to maximize the amount of information you can extract from your microscopy images.
Griottes is an easy-to-use, one-stop, Python library to extract single-cell information from your images and return the data in a networkx graph recapitulating the tissue structure.
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It works on segmented 2D and 3D images, no extra fuss required! We like to use CellPose for our image segmentation - but that's just a question of taste. You can also use dataframes as inputs.
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On both 2D and 3D images you can easily insert extra information from supplementary fluorescence channels and embed the information on the graph.
Griottes allows you to easily generate networks from your image data as shown in the image below.
For the moment, only installation via the repository is possible, so you'll have to download it from the command line. In the command prompt enter:
git clone https://gitlab.pasteur.fr/gronteix1/spheroid-graphs.git
This should download the project. Then install the required packages. In the terminal, navigate to the package directory and type:
pip install .
The library is now installed on your computer. An example of the library can be accessed here.
test_image # multichannel image
G = griottes.blablabla