Frequently Asked Questions

We have put together a list of some of the most frequently asked questions about our various product lines. If you are unable to find the answer to your question or need further assistance please reach contact us here, and one of our Plexon Sales Engineers will be in contact with you as soon as possible.

CineLyzer Behavioral Tracking and Analysis System

How do I set up my experiment database?

How do I set up events in CineLyzer?

How do I track behavioral files using CineLyzer?

CineLyzer with Multi-Fiber Photometry System

How do I set up my photometry system?

Can I place a credit card order?

  • Yes you can do so here.

What is your standard shipping method?

  • FedEx Express Saver (3-day) for domestic. FedEx International Economy for international.

Can you ship my order using expedited shipping?

  • We will ship according to the terms on your purchase order. If you need expedited shipping, please have purchasing approve this request in writing to Plexon.

How can I submit my order?

  • You can email purchase orders to or fax them to +1 (214) 369-1775.

Headstage Cables

Are headstage cables available in custom lengths? What is the maximum length I can get?

  • Headstages are available in custom lengths, the maximum length for a headstage cable depends on the type of headstage cable and the type of wire used. However, Plexon recommends using the shortest length possible for analog headstage cables. This is because the cables will act as antennas and increase the amount of noise picked up along the way.

Will increasing the length of my digital headstage cable increase noise in my signal?

  • No it will not.

Can you repair damaged headstage cables?

  • Unfortunately, repairing damaged headstage cables is not possible. The costs associated with the repair is nearly the same as the price of a new cable, in addition, repaired cables are typically noisier and more difficult to use.

Omnetics Connectors

Does Plexon sell the Omnetics connector I need?

What is the name of the connector for the NanoZ?

  • The NanoZ has two Samtec connectors.

What configuration file do I need to select in the nano-Z software drop down menu for use with my Plexon nano-Z adaptor? 

  • Make sure that the drop down menus for the adaptor and probe say “No adaptor” and “Probe not selected.” Please note that this only applies to nano-Z adaptors built by Plexon.

Does Offline Sorter work with Mac?

  • Offline Sorter is only compatible with Windows 7, 8, and 10

Can Offline Sorter be run on a virtual machine (i.e. dual-booting Windows on a Mac)?

  • Offline Sorter cannot be used on a virtual machine on a Mac. Offline Sorter is only compatible with Windows on a PC.

How do I change thresholds for my data?

  • Once you have the wideband data recorded, open the .pl2 file into Offline Sorter. You’ll see a table on the right side of the screen that looks a lot like an Excel spreadsheet. Scroll down until you see a “wide band” channel- likely labeled “WB & channel number”. Double click on the channel you want to select. That will make that the “active channel” and you should see the continuous trace along the bottom of the screen. To the left of the signal trace you can select a filter type on a drop down menu, select a cut-off frequency (e.g. 250Hz), adjust your threshold (blue or red horizontal line), and then click “Detect”.

Is Offline Sorter v4 capable of loading both .plx and .nex files?

  • Yes, Offline Sorter version 4 can load .plx and .nex files.

Is Offline Sorter v4 compatible with the neural data (.plx files) acquired through the MAP system?

  • Yes, Offline Sorter version 4 can load .plx files from the MAP system.

In the 2D plot is there a way to show every other, or every 10th spike?

  • To do this you can use the “Max w/f draw” setting (an in depth discussion can be found in the Offline Sorter User Guide, pg 43).

How do I save a file so that when opened, the sorted units appear on the continuous data? / How do I save a file such that all the data is preserved?

  • First, open your sorted file and select the channel with the sorted spikes, which will look similar to this.
  • The sorted results are there, but no continuous data. You will need to tell Offline Sorter to also show the continuous data. In the Channels window, scroll down to the channel of continuous data and right-click on the channel with the data you want to also view. Within the right-click menu is an option to “Also Show this Channel in Timeline View
  • Clicking this will add the continuous data to the Timeline.
  • One tip: You may have to click single-click on the continuous channel. Sometimes the “Also Show…” option is grayed out in the right-click menu. This may be because the continuous channel is not yet selected.

How do I create a topology with OmniPlex?

Can I record EEG/EMG/EOG/EKG/ECG etc. with a Plexon system?

  • Yes. In addition to the neural data channels that are processed through the headstage and front-end at 40kHz, the OmniPlex can be equipped with an auxiliary analog (AuxAI) subsystem. The AuxAI is capable of sampling up to 32 channels at 20kHz, and if needed, 4 channels at 250 kHz.

Does OmniPlex work with Windows 10?

  • No, OmniPlex is currently only compatible with Windows 7

Can I use my OmniPlex system to send out 5V TTL output to other equipment?

  • Yes, you can use the Plex DO SDK to send out TTL pulses from the digital out ports that are located under the BNC connectors on the AUX I/O subsystem in the front of the OmniPlex Chassis. You can find the Plex DO SDK here on our website under the “OmniPlex and MAP Online/Client“. You can use the bare wire digital input cable to connect the digital outputs to other equipment.

How can I measure electrode impedance? 

  • Impedance measurement can be accomplished many different ways. Plexon recommends using the NanoZ, a device made specifically for impedance and electrode plating. The NanoZ cannot work with OmniPlex, i.e. it is not possible to measure impedance while the electrode is plugged into the headstage. You can find out more here.

PlexBright Optogenetic Stimulation System

How do I set up my PlexBright Optogenetic Stimulation system?

How do I measure power outputs with my system?

Is it possible to interface with the light source through a third party controller, or do I need the optogenetic controller with Radiant?

  • The LEDs are driven by current so as long as you can control the current in a way that suits your needs then yes the LEDs can be driven by other third party systems.


What LED would I use if I wanted to activate a certain rhodopsin?

HELIOS – Wireless Optogenetic System

How do I get started with HELIOS?

What is the battery life of the LED?

  • The life of the LED battery depends on the power of the LED and the time it is on during the experiment. It can be recharged approximately 400 times, or last 2-3 years.

How many HELIOS devices can be used at the same time? How long is the working distance?

  • The number of HELIOS systems that can be used at a time depends on whether the experimenter wants the animals to receive separate stimulation patterns. Several HELIOS systems receiving the same stimulation pattern can be used at once, but the transmitters must be separated (with a barrier to IR stimulation) to control separate stimulation patterns. You cannot send two different stimulation patterns to the same area.
  • The working distance is approximately 2 feet, however, multiple transmitters can be used for larger arenas.

Will an infrared camera interfere with the HELIOS device?

  • If the infrared light has a frequency of infrared output that is similar to the HELIOS transmitter, then this will interfere with the HELIOS system.

How heavy is the HELIOS device?

  • The weight is 2.8g, which includes the battery.

How do I control the HELIOS device?

  • Control is via TTL, which means any device you have capable of sending out a pattern of TTL pulses should work. Alternatively, Plexon offers its own software-control device, which enables the user to create complex patterns of TTL outputs.

What wavelengths is HELIOS available in?

  • Blue – (465nm/300mA)
  • Green – (525nm/300mA)
  • Lime – (550nm/500mA)
  • Orange – (620nm/250mA)

Patch Cables

Should I use stainless steel jacketing for my experiment with mice?

  • Most of the time, mono-coil and stainless steel jacketed cables are too heavy for mice. The stainless steel jacketed cables are even heavier than the mono-coil cables.

Do patch cables come in custom lengths?

  • Yes, High Durability or High Performance cables can be made in custom lengths to the nearest tenth of a meter. The maximum length for High Performance patch cables is 2.3 meters, while High durability patch cables can be made in any length to the nearest tenth of a meter.

What is the difference between High Durability and High Performance fibers?

  • High Durability fibers have a lower numerical aperture than the High Performance fibers at .5NA, but may be more optimal in experiments in highly active animals. The High Performance fibers on the other hand have a numerical aperture of .66 with all glass construction, which makes it heat, chemical, and scratch resistant. The High Performance patch cable provides the highest possible output intensities from PlexBright LED Modules.

What is the benefit of magnetic fiber stubs? Are these available in both LC and FC?

  • Magnetic fiber stubs allow for rotational movement such as spinning and twirling at the connection in freely behaving animal experiments, reducing torque on the implant. These are only available with LC Ferrule tips. Also, the magnetic attachment allows for easier attachment of the patch cable to the fiber stub. View a video of this connection here.

How do ThorLabs and Plexon patch cables differ?

  • The main difference is in power output. The outputs reported on the ThorLabs website are substantially lower than those reported on ours. Part of this is due to the type of fiber used for the patch cables. Plexon uses a proprietary high-NA fiber to maximize the power output from our LEDs. If you look at our power outputs at the tip of a patch cable, you will get 3x the power with a blue LED module.

What is the difference between U, V, and S probes?

  • All three configurations are multi-use, multi-site linear electrodes, the difference being in their tips. The U-Probe is robust with a blunt tip angle and is most often used for acute studies with larger animals such as primates, while the S-Probe has a solid stainless steel tip and is the strongest of the three tip designs, similar to a sharpened pencil, and while not recommended for puncturing dura, customers who must do so may have better success with the S-Probe tip. The V-Probe has a tapered, conical-shaped tip for easier penetration and reduction of trauma upon entry, in addition this specialized tip permits the recording site to be closer to the tip of the probe.

What is the lead time for custom probes?

  • 4-6 weeks

What is the reinforcement tube for?

  • The reinforcement tube has two functions: 1) It reinforces or strengthens the junction between the thinner recording tube (where the electrode sites are) and the connector block, which is the interface to the recording headstage, and 2) it allows for a convenient connection point for the microdrive. Most probe users attach the microdrive to the reinforcement tube. The reinforcement tube is thicker in diameter than the recording tube, which allows for a strong connection point.

Where can the fluid capillaries be located?

  • Fluid channels can be placed between any two sites in a S or U probe. Fluid channels on a V probe must be placed in the first half of the sites closest to the connector.

How should I sterilize my probe before use?

  • We recommend ethylene oxide gas or UV sterilization. Alcohol is not a sterilant, but can be carefully used if EtOH or UV light is not available. However, the longer the probe – and specifically the tip – is exposed to alcohol the more likely the epoxy holding the wires in place will soften. While probes may be rinsed briefly with alcohol, they must be allowed to air dry immediately thereafter. The tips of the probe must not be allowed to sit in alcohol for more than 15 seconds as exposure to alcohol runs the risk of dissolving or damaging the epoxy which holds the electrode sites in place.

What is the inner and outer diameter of fluid channels on probes?

  • The inner diameter is 40μm and the outer diameter is 60μm.

Can’t find your answer? Ask us a question.