Dependencies: To-add.
Repository for UMAP project.
Matlab scripts and workflow:
- downsample : Downsampling of HPC and PFC signals to 2500 Hz.
- detection : Detection of ripple events.
- preprocessing: Ripple extraction, alignment, filtering, normalization and organization in a table.
Python scripts:
For the following steps, one needs to switch to python. Create a umap environment using the environment.yml file.
• flatcells: Function to accumulate values from Numpy array. It iterates across trials , extracts features of events and stacks them together.
• strcmp: Function to compare strings with numpy arrays. Output is a binary vector with 1 if the string matches.
• binary_feature: Returns a vector with True or False values indicating if a ripple meets some criteria. Usually used after strcmp.
• plot_umap: Plots the UMAP embedding including the labels of a specific feature.
• plot_binary: Takes as an input a binary vector indicating if the ripples meet some criteria. For example, do the ripples belong to Rat 9? The output is a density plot in the UMAP embedding.