We used to be able to obtain these data using Minianalysis, but the software recently stopped working on the lab computers. We believe this is due to an update of our computers. (This update was more or less against our will)
To extract the minis from the recording I strongly recommend using Eventer developed by Andrew Penn (Sussex) https://eventerneuro.netlify.app/
It's free and the other advantage is that it uses machine learning so it avoids bias and saves a lot of time. We've tested it with miniature events (inhibitory and excitatory and it works great!).
Quoting from download site:
"Eventer is a programme designed for the detection of spontaneous synaptic events measured by electrophysiology or imaging. The software combines deconvolution for detection, and variable length template matching approaches for screening out false positive events. Eventer also includes a machine learning-based approach allowing users to train a model to implement their ‘expert’ selection criteria across data sets without bias. Sharing models allows users to implement consistent analysis procedures. The software is coded in MATLAB, but has been compiled as standalone applications for Windows, Mac and Linux.
Eventer enables rapid, reproducible and unbiased analysis of synaptic events. To further aid in enhancing reproducibility across laboratories, this repository has been established to enable sharing of models trained across a range of model systems."
Winchester, G., Liu, S., Steele, O.G., Aziz, W. and Penn, A.C. (2020) Eventer. Software for the detection of spontaneous synaptic events measured by electrophysiology or imaging (Version 1.0.1). http://doi.org/10.5281/zenodo.3991677"
Also, from your question, not sure if you already have extracted the mini data from your recording (the instantaneous frequencies or the amplitudes) and just need to plot them? If so, you can plot them with most packages; eg. Graphad (frequency distribution) or Matlab (cdfplot).
Hey that’s a great tip Mariana! Definitely will look into that…
Another option for you Cody is to run minianalysis on a virtual machine that is operating a pre-update version of your lab computer, which is what we’re doing at the moment.
Dear Dr. Boyle,
I have a mini analysis program that you can download from my Researchgate page. It works with ABF files and it is much faster then MiniAnalysis. The link to the page is:
Method Analysis of miniature excitatory postsynaptic currents (mini...
Let me know if you have any questions. If you have one membrane current channel and one holding potential channel and the sampling frequency is between 5 and 50 kHz, it should work. If the program does not load the file, you can send to me a sample file and I can find the reason.
Best regards, Attila Szücs
Dr. Szücs,
Thank you very much! I will see how this works and let you know if any questions come up.
Kind regards,
Cody Boyle
- Badges
- Science topic
- Similar topics
- Computer Science and Engineering
- Programming Languages
- Python