STROBE and SPC Seminar – Hands on Python Workshop: Image Analysis in the Jupyter Notebook

Workshop Materials

This hands-on workshop will give students a taste of modern scientific computing in python using the Jupyter Notebook environment. Jupyter notebooks are executable documents that interleave narrative (rich text, math equations, figures, links) with code. The notebook workflow ties together high-level descriptions of the analysis, code and results in a single document that is easy to share or re-run. Even beginners can read and re-run analyses modifying parameters and exploring the effect on the results, either on the cloud or on personal computers. In this workshop we will interactively explore a single-molecule fluorescence microscopy video, performing tasks such as background subtraction, denoising, region of interest extraction, segmentation and analysis of blinking time-trajectories (on-off trajectories) of individual emitters. We will use numpy, scipy, matplotlib, pandas and more. Some basic experience with python is preferred. The analysis will be performed on a cloud service accessed with own laptop (browser-only, no installation required).All participants are required to register and test the login prior to the workshop. Users without a working log-in will not be able to participate.

For registration go to:

We would like to thank Max Kopelevich for IT surpport involved with this workshop. We also would like to thank Yung Kuo and Maya Segal who served as instruction assistants for the workshop.


Feb 26 2018


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