CinePlex 3.5 Digital Video Recording/Tracking

Plexon’s newsletter from May 29, 2014 CinePlex3.5, Neuroexplorer V5, and other Plexon behavioral research systems.


May 29, 2014

CinePlex® 3.5 with Freezing Detection Released

Good news for labs using video recording – CinePlex® Behavioral Research System software version 3.5 (CinePlex System) is now available on the Plexon website.

The CinePlex System is possibly the industry’s most advanced approach to digital video recording, position tracking and behavioral analysis for freely moving and behaving animal experiments. Further, Plexon’s CinePlex System is the only behavioral research system that can either be operated in full synchrony with neural data acquisition, or as a stand-alone solution.

Since the last release, the development team has dedicated countless hours not only to expanding functionality, but also simplifying the interface, refining the algorithms and improving the performance. The result is an easier to use system, yet unexpectedly with more granular control of data capture and analysis. Some of the more significant additions include freezing detection, support for more economical cameras and the significant expansion of multi-camera support.

Freezing detection is especially valuable in learning and memory research, most specifically for fear conditioning studies. CinePlex System v3.5 now empowers researchers to avoid the tediousness, variability and low throughput nature of manual scoring by confidently automating the detection and resulting calculations. The user can average the motion measure, set the freezing threshold, span gaps if desired, and then generate markers around the resulting freezing episodes. Multiple sets of detected episodes can be created with varying parameters, reviewed, modified if needed, and saved for future analysis.

CinePlex System v3.5 now also offers the researcher operating CinePlex in the stand-alone configuration a more economical camera option with Point Grey Firefly cameras while still maintaining good quality. Taking camera features a step further, the new release supports calibration in one or two dimensions, as well as speed measurements and events for multiple cameras.

This latest download can be found on the CinePlex System webpage as well as at under the CinePlex Behavioral Research System header.

For more information regarding these or other improvements, consult the CinePlex Change Log or contact

JoVE/PlexBright® Contest Deadline Saturday

Plexon/JoVE Publication Grant Contest focused on research performed using the industry leading PlexBright® Optogenetic Stimulation System closes on May 31, 2014 at 11:59 p.m., Central time.

Previous winner, Jonathan Ho of Rebecca D. Burwell’s Behavioral Neuroscience of Memory and Attention Lab at Brown University, shares his perspective regarding the contest and winning:

“What I took away the most from this experience was that Plexon is genuinely interested in our research and wants to provide us with the best platform to carry out our work. I now consider Plexon as an important partner in our research rather than simply a company supplying our equipment. Winning Plexon’s contest gave us the fantastic opportunity to showcase our research and experimental protocols using Plexon’s products to a wide audience through JoVE’s unique publication media.

The partnership between Rebecca Burwell’s lab and Plexon has no doubt been strengthened from this positive experience, as have individual professional relationships, which will undoubtedly be an advantage in future endeavours. Our partnership enables us to have an open dialogue with Plexon to suggest improvements and developments to their already excellent products that would suit our ongoing research needs. More importantly, strong partnerships like this result in continual innovation in both research and technical means to tackle the infinite questions neuroscience poses.”

Plexon truly values the experience with Dr. Burwell’s lab, whose article titled “Automated Visual Cognitive Tasks for Recording Neural Activity Using a Floor Projection Maze” has now reached nearly 1,400 views from approximately 30 countries, and looks forward to being a catalyst in launching another innovative research group into the international spotlight.

For more information, the Official Rules or to download the application, visit

NeuroExplorer® v5 Available June 30

Plexon announces the much anticipated launch of NeuroExplorer® version 5.0 in less than five weeks! NeuroExplorer is a neurophysiological data analysis package that supports sophisticated analyses and generates professional presentation of the results. It is the undisputed industry gold standard in data analysis programs cited by more than 1,700 scientific publications.

Version 5 is a truly significant expansion of functionality over the previous version – seven years in the making! Some of the most significant advances include:

  • Vastly improved spectral analyses of spike trains and continuous channels including single taper and multi-taper calculations of spectra, six available windowing functions, three preprocessing options, jackknife confidence, the ability to replicate MATLAB® spectral calculations, up to 10 times faster calculation of spectral results, and more.
  • New analyses of continuous data (LFP) such as perievent rasters, power spectra, coherence, single trial spectrum analysis, and phase analysis using Hilbert Transform.
  • New digital filtering options for continuous data including seven new IIR and FIR filters.
  • New spike train analyses featuring firing rate versus head direction, and single trial rate estimation via adaptive kernels.
  • New statistical tests (T-tests, Wilcoxon tests and ANOVA) can compare results across conditions that can be implemented via integration with R-script. New statistical tests can be also be added by users by writing R-scripts.
  • Immediate preview of data when a data file is loaded.
  • New 64-bit build enabling NeuroExplorer v5 to load and analyze multi-gigabyte data files, and display hundreds of millions of rows.
  • Supporting the new .NEX5 data file format that is more flexible than the previous .NEX format such that it allows saving files greater than 2GB in size, and saves unlimited metadata for the whole file and for every file variable in JSON format.
  • Enhanced ability to save and restore results such that it saves all numerical and graphical results in a series of linked files, and a user can open results files without recalculation, as well as replicate results.
  • More efficient processing as computationally demanding analyses are run in parallel using all CPU cores.
  • Localized language such that any language can be used in file names, file comments and variable names.

For a quote with NeuroExplorer v5 single or three-seat licensing packages, or for upgrades from any prior version of NeuroExplorer, contact

Plexon – the Lead Sponsor of the NIC

Plexon is thrilled to have an opportunity to demonstrate its strong support as the only Platinum+ sponsor for the 41st Neural Interfaces Conference to be held in its home city of Dallas, Texas, USA in collaboration with the Texas Biomedical Device Center and the Department of Biomedical Engineering in the Erik Jonsson School of Engineering and Computer Science at the University of Texas at Dallas (UTD). We are especially pleased to partner with Robert Rennaker, PhD of UTD as the Conference Chair and Joe Pancrazio, PhD of George Mason University as the Steering Committee Chair to host an anticipated crowd of 400 scientists.

As the lead sponsor, Plexon will also sponsor the Tuesday evening dinner at the acclaimed Perot Museum of Nature and Science beginning at 7:30 p.m. – an event not to miss! The museum opened its doors December 1, 2012 and welcomed its millionth visitor just eight months later.

Attendees are invited to Plexon’s island booth to be amongst the first to see the PRE-LAUNCH OmniPlex® D2 Neural Data Acquisition System platform for use with Plexon’s new digital headstages. Researchers will also have an opportunity to work with the PlexBright Optogenetic Stimulation System, the CinePlex Behavioral Research System, the industry-standard Offline Sorter Software, and even have an advanced peak into the new NeuroExplorer v5 to be launched June 30th.

Workshop Registration Raffle at NIC

Due to popular demand, Plexon will once again host a Workshop Raffle – this time at the NIC. We will raffle off a FREE REGISTRATION to the very popular, intense, multi-day, hands-on 2015 Annual Neurophysiology and Behavioral Research Workshop in which the winner will receive a full registration valued at $900.00. Earlier this year, the attendees rated the 2014 event an outstanding 9.5/10!

Checkout the green sidebar to see what Yuichi Makino, PhD from the Department of Molecular & Cellular Biology at Harvard University had to say about his experience at the Plexon Workshop.

Raffle contestants are invited to enter once during the opening hours of the 41st NIC at the Plexon booth. Contestants can be any researchers in attendance that are not distributors for, employees of, or in any way agents of Plexon Inc. Upon the close of the exhibition, the winner’s name will be drawn and he/she will contacted shortly thereafter.

Contact with any questions. Good luck to all raffle contestants!

Did you know . . . How to Upgrade Plexon License Keys?

A number of software products offered by Plexon require a license key for full operation, such as Offline Sorter or NeuroExplorer. New software releases within a version (such as v3.1 to v3.2) are available free of charge and can simply be downloaded from the Plexon website. These minor releases do not have an impact on the license key.

However, when incrementing from one software version to the next (such as v3 to v4), the license key itself must be upgraded. License keys are upgraded using a proprietary program called PlexLicTool and special key serial number-specific codes generated by Plexon. It is important to note that not all Plexon license keys can be remotely upgraded. Only the black, USB keys are upgradeable, while all others will need to be exchanged.

The process to upgrade your black, USB license key is as follows:

1) Identify the serial number for each license key needing to be upgraded (found on the license key label or electronically read from key using PlexLicTool),
2) Email with the serial numbers, the name of your institution, first and last name of the Principal Investigator, and request a quote for the specific software upgrades desired,
3) Make the purchase with a PO or via credit card,
4) Download the most current version of PlexLicTool (Plexon License Key Upgrade Package) from /software-downloads under the Utilities Header.

When Plexon responds with the upgrade codes, plug the first license key into a computer and launch PlexLicTool. A window will appear populated with information specific to your key on top and displaying four open fields at the bottom (if not, contact Enter the four license key-specific codes provided by Plexon in the corresponding fields numbered one through four. Click Enter Code to accept, then click OK, then click Done when prompted. The license key was successfully upgraded. Repeat for each key you wish to upgrade.

Research Spotlight

Let us know about your 2014 publication citing Plexon and our equipment and we will send you a thank you award with a mug and a T-shirt! Send notices, address and T-shirt size to

All articles listed are alphabetical based on first author within two categories: articles published online in electronic-only journals or ahead of print, and articles published in full print.

Recent articles published online in electronic-only journals or ahead of print:

Recent articles published in full print:


Plexon Workshop Alumni Speak Out

“I just joined a lab that uses a couple of Plexon recording setups. I had absolutely no experience in using the Plexon system before joining the lab, so I had to struggle for figuring out how the entire system works. I could get a tremendous help from the Plexon workshop because there I could learn every detail of the Plexon system – what each part of the hardware means, how they are assembled to work together, how to use each function of the software and for what kind of purpose, etc. – on a very very hands-on style. Now I am back to the lab and am much more comfortable about using our system. I would definitely recommend this workshop to anyone who uses the Plexon system, but particularly to the people who are new to it.”

Yuichi Makino, PhD
Department of Molecular & Cellular Biology, Harvard University

Register for 2014 China Workshop

July 22-24, 2014 at the East China Normal University in Shanghai. Contact for more information or to register.

Office Closures

In honor of Independence Day, Plexon World Headquarters will be closed Friday, July 4 and will reopen for business on Monday at our standard business time. See annual office holidays for the US and European offices for additional closures throughout the year.

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PLEXON®, the five-line symbol, CereStage™, CinePlex®, DigiAmp™, MiniDigi™, Offline Sorter™, OmniPlex® PL2™, PlexBright®, PlexDrive™, Radiant™, and RapidGrid™ are registered and
unregistered trademarks of Plexon Inc, Dallas, Texas, USA. ©2014 Plexon Inc. Other product and company names mentioned are trademarks or registered trademarks of their respective owners.