The Stimfit book of spells¶
19 August, 2021
This document collects answers to some questions like “How do I make … in Stimfit with python?”. Though much of the material can be easily found in the Stimfit manual, the examples provided here are a good way for the casual user to start using Python in Stimfit.
It assumes a basic knowledge of the embedded Python shell of Stimfit. Some Python knowledge and a substantial proficiency in Stimfit are recommendable. Please note that this is not a Python manual, but a way to use Python for some basic analysis tasks provided with Stimfit. For a detailed Python manual, we encourage the user to visit the official Python documentation on the [Python-website] and to read carefully the Stimfit manual.
>>> import spells
After that, functions can be called with the dot notation (i.e just typing spells before the function) For example, if we want to call the function rmean() we would do it in this way:
Finally, the contents of this document are organized with increased level of complexity, assuming some of the last chapters concepts and topics described in the first chapters. Thus, we encourage the newcomer to follow the order exposed below or to visit the section code commented in previous chapters.
- Resistance Calculation
- Running mean
- Calculations on selected traces
- Cutting traces
- Event counting
- Object oriented programming with Stimfit
- Calculating latencies
- Loading custom text files