RESOURCES
We are committed to open science and believe that the standardization and disseminations of data and tools is an important way to advance Neuroscience. In the near future we will update this section with neural data analysis tutorials and documented datasets, so come back soon!
Software:
- Buzcode: A Matlab toolbox for the analysis of behavioral and electrophysiological data. It is under constant development by current and past members of the Buzsaki lab. Much of our own codes for LFP, spikes and behavioral analysis are part of it.
- Neuroscope: Viewer for neurophysiological and behavioral data: it can display local field potentials (LFPs), neuronal spikes, behavioral events, as well as the position of the animal in the environment. Very useful for streaming LFPs recorded with Intan in real-time.
- CellExplorer: Matlab graphical user interface (GUI) for exploring and classifying single cells acquired using extracellular electrodes developed by Peter Petersen in the Buzsaki Lab.
- Kilosort: MATLAB package for spike sorting of large-scale electrophysiological data developed by Marius Pachitarius. Our favorite spike-sorting software!
- Phy: Nice interactive visualization and manual spike sorting python GUI to curate and refine the output of Kilosort.
- DeepLabCut: Python toolbox for markerless pose estimation of behaving rodents and any other animal.
Datasets:
Part of our published, and some unpublished, data is already publicly available (check links below), and more will soon be added. We are working in preparing several datasets that will be shared in this web page. Contact us if you are interesred in something specific, we are always looking forward to new collaborations.
Tools:
- Silicon probes: We use silicon probes from various sources including Neuronexus , Cambridge Neurotech and Diagnostic Biochips to record single cells and LFPs in behaving animals. You can find in their catalog several of our custom designs. Silicon probes with integrated uLEDs for focal optogenetic stimulations are manufactures by Neurolight .
- Neuropixels: High-density CMOS active probes with ~1000 channels per shank.
- Custom made micro-drives and head implants: We use various custom designs for micro-drives and head implants that can be 3D printed. The most up to date version is described in this recent publication: https://elifesciences.org/articles/65859
- Miniscope: One-photon mini-endoscopes for calcium imaging of large neuronal ensembles. There are several versions but we use the open-source UCLA miniscopes and NINscopes .
- Intan / OpenEphys: Intan Technology manufactures large channel count (256-1024) affordable digital acquisition systems.