MRBLEs decoding and analysis package
Project description
This project aims to provide a package to find, decode, extract, analyze and MRBLEs using a set of images.
This package provides the tools to: (1) find the MRBLEs in a monochrome brightfield microscopy image; (2) decode the MRBLEs beads by spectral unmxing, using reference spectra, and then spectrally decode the found beads using Iterative Closest Point Matching and Gaussian Mixture Modeling; (3) extract, statistical values of interest in additional fluorescence channels using the morphology of the MRBLEs, their locations, and respective code; (4) analyze affinity information based on titrations of MRBLEs assays.
MRBLEs project
MRBLEs (Microspheres with Ratiometric Barcode Lanthanide Encoding) rely on spectral multiplexing to track analytes throughout an experiment. In these assays, we can create microspheres containing > 1,000 unique ratios of lanthanide nanophosphors that can be uniquely identified via imaging alone. We are currently developing new assays that use these microspheres to understand how signaling proteins recognize their peptide substrates and to improve our ability to extract information from single cells.
Links
Documentation: https://fordycelab.github.io/MRBLEs/
Source code: https://github.com/FordyceLab/MRBLEs/
Installation
The MRBLEs software package is a Python Package available through the Python Package Index (PyPI): https://pypi.org/. To makes us of mrbles follow the following instructions:
- mrbles is built to be compatible with Pyhton >2.7, but its dependencies (other Python Packages) are getting less and less support for Python 2.7.
Detailed Windows installation: https://docs.python.org/3/using/windows.html - Must have C++ compiler installed to be able to install package from source code. See link above. - If using Python 2.7, also install Microsoft Visual C++ Compiler for Python 2.7. - If using Python >3.6, also install Build Tools for Visual Studio 2017. - More info on compilers here.
Detailed MacOS installation: https://docs.python-guide.org/starting/install3/osx/#install3-osx - Must have XCode (or other C++ compiler) installed to be able to install package from source code. See link above.
During installation make sure to tick the box “Add Pyhton 3.x to PATH” (Windows) or manually add Python root and Scripts to system path.
Once Python is installed it can be accessed using your systems’ terminal, using:
> python or > python3 depending if only Python 3 installed or both Python 2 & 3.
Now the mrbles package can be installed, using the following command in the terminal (exit Python environment first, or start a new terminal):
> pip install mrbles or > pip3 install mrbles depending if only Python 3 installed or both Python 2 & 3.
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