This repostory contains material for the STROBE seminar that will be held on Feb. 26th 2018 at UCLA, and in videoconference with UC Beckley, CU Boulder and UC Irvine.
During this workshop we will get the hands dirty analyzing the blinking trajectories of a single-molecule fluorescence microscopy video. We use the Jupyter Notebook environment with Python 3.6 and common scientific packages (Numpy, Scipy, Pandas, Matplotlib and Seaborn).
To save time, partecipants will use a dedicated JupyterHub server with all the software already installed. The only program needed is a web browser to connect to the server. However, we will shut-down the server a few days after the workshop. So, if you want to run again the analysis you need to install the software on your own computer and download the data and notebooks from this repository.
To install the Python and Jupyter on your own computer, we recommend installing the Anaconda Scientific Python Distribution which includes the important packages for scientific computing with Python. All the software is free and open source and multi-platform (Windows, Linux, Mac).
This repository contains notebooks and data files used for the workshop.
Please get familiar with Numpy indexing before the workshop by reading and running the notebook:
- Numpy Primer: a short primer on numpy
- Fluorescence Blinking Analysis: the notebook used to analyze the fluorescence video.
You will find the same notebooks in the Jupyter sever after you login.
Many thanks to Xiyu Yi for providing the simulated data used for this workshop.
The material here posted is released in Public Domain (CC0). For the material referenced (for example the cheatsheets) check the license of the original material (links in the notebooks).