Description:
OPIPP 0.1.1
OPIPP: Optimization-based Pairwise Interaction Point Process
A Python implementation of OPIPP, a method for precisely generating artificial retinal mosaics, the spatial organization of retinal neurons. Here is a short introduction to the background.
Pipeline
We recommend the "import-analysis-simulation" pipeline for generating artificial mosaics and purpose a tutorial for each step, as
Importing retinal spatial pattern datasets from local files
Analyzing and visualizing spatial patterns of mosaics
Simulating artifical retinal mosaics
Users are welcome to extend and customize methods for feature calculation and mosaic simulation.
Tools
Here are useful tools that are not implemented in the current version. We plan to apply these methods in future development.
Estimate parameters of mosaic simulation by R
Parallel process for mosaic generation by MPI
Install
PyPI (pip)
pip install git+https://github.com/heliy/OPIPP
Dependencies
python >=3.8
numpy >= 1.20.0
scipy >= 1.9.0
matplotlib >= 3.2.0
networkx >= 2.0.0
Citation
TODO
References
The example mosaic for retinal horizontal cells and related spatial features are from (Keeley et al., 2020).
In the optimization, we use the adaptive simulated annealing algorithm from (Ingber, 1993).
License
For personal and professional use. You cannot resell or redistribute these repositories in their original state.
Customer Reviews
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