Electrode Pooling Data and Code
MM 7/12/2021
This repo accompanies our preprint
[Kyu Hyun Lee, Yu-Li Ni, Jennifer Colonell, Bill Karsh, Jan Putzeys, Marius Pachitariu, Timothy D. Harris, and Markus Meister (2021) Electrode pooling: boosting the yield of extracellular recordings with switchable silicon probes. BioRxiv 851691.] (https://www.biorxiv.org/content/10.1101/851691v2)
It contains all the data and code needed to reproduce the published analysis.
Contents of the repo
-
Jupyter notebooks (Python) and m-files (Matlab):
Theory
,Saline
,Invivo
,Simulation
,Simulation_Fig
,accuracyQC.m
. These notebooks develop the various topics of analysis, starting from raw data, producing figure panels and numerical results for the article along the way. They contain a good number of comments and mathematical sections to guide the user. -
code/
: Contains routines accessed from the notebooks. -
data/
: Data files, both input and output. -
figs/
: Image files that make up the figure panels in the article.
How to reproduce all the analysis starting from raw data
- Read our paper. A version from May 3, 2021 is included in the repo.
- Empty the
figs/
directory. - Run the notebooks and m-files in this order:
Theory.ipynb
- Fig 2Saline.ipynb
- Fig 4, Fig 8Invivo.m
- Fig 5Simulation.m
- Fig 6Simulation_Fig.ipynb
- Fig 6accuracyQC.m
- Fig 9
- Now the
figs/
directory should contain all the figure panels.
How to find code for a specific figure panel
- The names of all the figure panels (as numbered in the preprint) appear as headings in the Jupyter notebooks. Look through these to find your figure of interest. Or...
- In the
figs/
directory find the name of the figure file of interest, and search for that name in the Jupyter notebooks or m-files.
Simulation details (optional)
The m-file code/fig_6B_code/main_genSimulation.m
creates samples of voltage traces for simulated pooling, with parameters of Amp, Firing rate, and Noise.
Compatibility
Matlab code was tested on Matlab version R2020b
.
Jupyter Notebooks were run on MacOS using Python 3.8.