pyErmine 0.1.2

Estimate Reaction-rates by Markov-based Investigation of Nanoscopy Experiments (ermine) using Python.

pyErmine

Estimate Reaction-rates by Markov-based Investigation of Nanoscopy Experiments (ermine) using Python.

Author

Sebastian Malkusch

Data Science | Clinical Pharmacology
Institute for clinical pharmacology
Goethe-University-Hospital
Frankfurt am Main
Germany

Abstarct

The python package pyErmine analyzes the mobility of laterally diffusing molecules, such as membrane receptors, using hidden Markov models. It maps the movements of individual receptors to discrete diffusion states, all of which are Brownian in nature. The model is trained with single-particle tracking data.

Requirements

• hmmlearn >= 0.2.4
• numpy >= 1.19.2
• pandas >= 1.1.5
• scikit-learn >= 0.23.2

Reference

Publication in progress.

Tutorial

A tutorial including a test data set can be found on Github at the following repository: https://github.com/SMLMS/ermine-tutorial