Highlights from “NeuroExplorer 5.017, 120 Chinese Researchers, 2016 Workshop Dates, Dura Penetration with Probes and More!”
Save Huge Files with NeuroExplorer v5.017 – New Release
NeuroExplorer® – the undisputed industry gold standard in neural data analysis programs cited by more than 2,100 scientific publications – releases v5.017 enabling maximum flexibility when working with and saving neural data files greater than 2 GB and a new “Find Oscillations” analysis.
NeuroExplorer launched its new .NEX5 file format last year to meet the growing data demands of the industry. This most recent release leverages the increased flexibility of the .NEX5 format not only to analyze and save extra large files, but also to save unlimited metadata for the whole file and for every file variable in JSON format.
The main structure of the .NEX and .NEX5 file types is the same. The file starts with the file header followed by the variable headers containing data offsets. Binary data arrays are written after all the headers. The .NEX5 headers the contain minimum information needed to store, load and properly interpret data. The metadata that is less often used in analysis (for example, recording start time, recording software, electrode location, etc.) is stored in a string at the end of the file after all the binary data. Most importantly, the upper file size limit of 2 GB has been removed all together.
Another important advance in this release includes the “Find Oscillations” analysis which identifies episodes of oscillatory activity in the specified frequency band in recorded analog signals. The algorithm
is described in Klausberger, Magill, Marton, Roberts, Cobden, Buzsaki and Somogyi. Brain-state- and cell-type-specific firing of hippocampal interneurons in vivo. Nature, 2003 Feb 20;421(6925):844-8. The user specifies two frequency bands (for example, theta band and delta band). NeuroExplorer finds the segments of LFP signal where theta to delta frequency power ratio exceeds a certain threshold. The LFP signal is then band-filtered and oscillation cycle start times are identified via Hilbert transform. This analysis adds several new variables to the data file.
This latest release is available online at no charge for anyone with a NeuroExplorer v5 license key. Additionally, researchers will find supporting files for use with C++ and MATLAB® in the same location. More information can be found on the NeuroExplorer webpage or contact info@plexon.com.
Did You Know . . . How to Protect Your U- or V-Probe When Penetrating the Dura?
Plexon’s U-Probes and V-Probes are capable of recording in the rodent brain, as well as both deep and superficial brain structures in the primate brain. The procedure for safely penetrating the dura is different for each situation. It is very important to strictly adhere to these procedures to avoid damaging the tip of your probe.
Choose a sharpened guide tube that has an inner diameter that is 100-200 µm larger than the outer diameter of the thin section of the probe you are using. Only the thin section of the probe should enter the guide tube – not the reinforcement tube near the connector.
For targeting deep structures in the primate brain, first insert a sharpened guide tube through the dura and into the brain. The probe should be safely inside the guide tube during this procedure. Then pass the probe through the sharpened guide tube.
For targeting primate superficial cortex, insert a sharpened guide tube partially into the dura, but without puncturing the dura. Then pass the probe through the end of the guide tube and attempt to push through the dura. View the thin section of the probe that is visible above the guide tube during this process. If you see bending or flexing, stop immediately and pull back the probe as this is a sign that the dura is too thick and hard for the probe to pass.
For targeting structures in rodent brain in acute, head-fixed recordings, make a craniotomy. You may or may not wish to remove the dura surface. Then pass the probe vertically into the brain under stereotaxic control.