The latenZy repository is a Python and MATLAB toolbox containing two non-parametric, binning-free methods for estimating the onset of neural spiking activity with high temporal precision: latenZy and latenZy2. These methods leverage the cumulative distribution of spike times to detect time-locked changes in neural firing without relying on predefined time bins. Through an iterative process, they identify statistically significant changes … Read more
There are many options for spike sorting, which are continuously updated and improved. Let us know (or create an account and edit) if you know of new options. IRONclust Kilosort 4 Mountainsort SpyKING Circus YASS A spike sorting pipeline in which spike sorters can be included SpikeInterface
For the acquisition of the data coming directly from the Neuropixels probe, there are two packages: SpikeGLX Open Ephys GUI There are a number of pipelines available for the whole process of Neuropixels recording. Here is a non-exhaustive list. Acquipix at https://github.com/Herseninstituut/Acquipix. This is a Matlab based pipeline to run experiment, building on SpikeGLX. It … Read more
Manual curation of electrophysiology spike sorted units is laborious and difficult to reproduce. See this talk at the annual Neuropixels course about quality control. There are tools to help. Bombcell Bombcell is a powerful toolbox that addresses this problem, evaluating the quality of recorded units and extracting essential electrophysiological properties. Bombcell can replace manual curation or … Read more
This page provides an overview of solutions for electrophysiological data storage and recall. We should strive to store neuroscience data comforming to FAIR principles. Ideally, researchers can easily find and access the data acquired by others. Many laboratories and vendors have their own data formats. There are a number of well-document data storage solutions that … Read more
Electrophysiological experiments often require determining the neuroanatomical location of a recording probe when it was inserted in the brain. Using probe trajectory reconstruction, one can use histological slices to estimate where in the brain neural signals were recorded. The classic approach is to align a histological brain slice to a stereotactic atlas and manually designate … Read more
Eye-tracking is common technique in visual neuroscience, where the position and size of the pupil are recorded with a video. The position of the eyes can influence neuronal responses, while the size of the pupil correlates strongly with noradrenaline release and the level of behavioural arousal. Several open-source eye-tracking programs are available, such as: … Read more
A common procedure in pre-processing neural data is removing cells that are not responsive to an experimental stimulus. Many experimenters determine the ‘stimulus responsiveness’ of a cell by comparing its average spiking rate during the presentation and absence of a stimulus (see Figure 1A–C for an example V1 cell). This procedure will therefore remove neurons … Read more
This toolbox was created to work with SpikeGLX to detect the location and size of a pupil. It will run online pupil detection during video acquisition, and automatically synchronize videos by creating a lookup table that logs pairs of SpikeGLX timestamps with video frame numbers. It also provides easy functionality to extract light pulses in … Read more
Whenever you perform electrophysiological recordings, you want to know which area you recorded from. While some great tools exist, the Universal Probe Finder allows you to fine-tune the probe location using electrophysiological responses. You can align your histological slices in 3D (Figure 1), and find the anatomical boundaries of brain regions along your probe (Figure … Read more