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This framework allows to perform scRNA-seq-like analyses of imaging mass-spectrometry data. Check out the example jupyter-notebook in examples/
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mjoppich/pIMZ
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pIMZ is a framework for Imaging Mass Spectrometry (IMS) data analysis.The python implementation is available fromgithub.com/mjoppich/pIMZ.For installation follow the instructions given here.
pIMZ focuses on a differential setting, where masses, specific to certain areas are first determined, and then serve as input for a cell-type detection framework and/or a differential expression setting.
pIMZ's documentation is available here: .
The easiest way to install most Python packages is viapip.
If not already done, you must first install the following dependencies manually. This is because at the time of writing this document, dabest requirespandas~=0.25, which is incompatible with probably the rest of the world nowadays. So first dabest is installed, then numpy and pandas are upgraded again ::
sudo pip3 install dabestsudo pip3 install numpy pandas --upgradeOnly then we should installpIMZ :
sudo pip3 install pIMZpIMZ is now ready to go!
References to examples and example notebooks can be found in theexamples folder, or in thedocumentation.
All available classes and their functions are explained in themodules/API documentation.
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This framework allows to perform scRNA-seq-like analyses of imaging mass-spectrometry data. Check out the example jupyter-notebook in examples/