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LernerLab / GuPPy

Guided Photometry Analysis in Python, a free and open-source FP analysis tool.
GNU General Public License v3.0
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Flow diagram of GuPPy trace processing #16

Closed matiasandina closed 1 year ago

matiasandina commented 2 years ago

Hello, I am doing a bit of analysis to make comparisons between different methods for fiber photometry analysis. I have noticed all methods are all very similar but with slightly different flavors. There is also more than one option on each pipeline. You have some hints on the wiki, and there's a figure on the paper with the traces, but I was wondering if you had a diagram or something sequential, closer to code with the parameter values, so that I can implement the same functions in the repo outside GuPPy to compare pipelines. If not, I am happy to make one but I would need a bit of help with the order of function calls :smile: !

venus-sherathiya commented 2 years ago

Just for more clarity, are you talking about methods used in "Step 4 : Extract timestamps and its correction" ? if not, can you please tell me which different methods you are talking about ?

matiasandina commented 2 years ago

Hello, sorry for not being clear. In the Figure 2 of the paper you have a diagram of the steps from raw signal to the final product. I was hoping to have something closer to code. I can go through the functions in preprocess.py and try to figure out the order in which they are called. Even something like Raw Data -> function1(params) -> function2(params) -> ... would help.

venus-sherathiya commented 2 years ago

Sorry for late reply !! Please try to look at "extractTsAndSignal" function in preprocess.py file. It's very easy to follow. Let me know if you find hard to get it, I will try to give you more details.