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
Multi-stream data recorded while performing a visual or optogenetic experiment, can be difficult and laborious to process. If your data includes stimulation, multi-channel spiking, LFPs, running speed, and pupil tracking, you will likely already have to deal with 5 independent data streams that need to be synchronized (fig. 1). Moreover, keeping track of all these … Read more