Dear all,
I would like to start a discussion and sharing of resources and knowledge on the use of Python for the analysis of ephys data. For the past years I have used Igor Pro and am very eager to migrate to Python as it is free, open-source and has many toolboxes available.
After a little research I found a package called Neo (http://neuralensemble.org/neo/). Does anyone know good packages to analyze voltage- or current-clamp recordings? EPSCs, mini EPSCs and such?
Furthermore, are there any packages or resources for Python that you deem worth sharing with the ephys community?
Thank you for your support
I use Neo to import .abf files and then I analyse manually with numpy passive properties, active properties and evoked synaptic responses. A tool worth sharing in that context is probably Elephant (http://neuralensemble.org/elephant/), which is also from the neuralensemble ecosystem. I tried it a while ago, didn't warm up to it and did everything in numpy but maybe it is worth another look. I am sharing it mainly because I use Neo and Elephant is the recommended package to analyse Neo data structures as far as I understood.
I am not a minis expert but it should be easy enough to extract them by threshold from a properly filtered signal (https://docs.scipy.org/doc/scipy/reference/signal.html) and then either manually accept/reject them based on waveform or cluster and exclude outlier waveforms. However, I am not entirely sure if that is still good practice in the minis field.
Stimfit was designed for this: https://www.frontiersin.org/articles/10.3389/fninf.2014.00016/full
I do not use it, so I cannot tell you if it's good or not, but might be worth a try.
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