SiNAPS Manual

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SiNAPS probes digitise at the electrode. Each site is an active pixel, so the signal is converted on the shank rather than carried out as an analog trace — which is what makes full-band recording from every site at once practical.

A SiNAPS system has four parts. The probe carries the active pixels. The SiNAPS interface box generates the control signals the probe needs. The SmartBox Pro is the acquisition system the interface box connects into. Allego configures the hardware, streams the signals and records them.

This manual covers what is specific to SiNAPS. The software it runs on is documented once, in the Radiens Manual ↗ — this manual links there rather than repeating it.

What's in this manual#

• Hardware — the two boxes, panel by panel, and every cable in the kit
• Setup — cabling order, computer requirements, installing Allego, confirming the connection
• Firmware update — reprogramming the interface box FPGA
• Calibration — the wet test, run it before every experiment
• In vivo — insertion, calibration in tissue, and the practices that keep a recording clean
• Troubleshooting — symptom, cause and fix, on the bench and in vivo
• Software — where the Allego documentation lives
• SiNAPS Probe Maps — site numbering for all three probes, a separate page

Hardware#

A SiNAPS system is two boxes and four cables. The probes are ordered separately.

SmartBox Pro#

The acquisition system. It uses a 9 V AC power adapter.

Front panel

Back panel

SiNAPS interface box#

Generates the control signals the SiNAPS probes need. It uses a 5 V AC power adapter — not the SmartBox Pro's 9 V adapter.

Front panel

Back panel

Cables and adapters#

SiNAPS–SmartBox Pro HDMI cable. Interface box to port A of the SmartBox Pro.

SiNAPS probe interface cable. Terminates in an IST-2mm connector with a bracket that holds the SiNAPS probe package. The mezzanine adapter must be fitted to it.

Mezzanine adapter. Connects between the probe interface cable and the probe package.

Blue USB 3.0 cable. SmartBox Pro to the computer. The same cable reaches the FPGA board during a firmware update.

Setup#

Connect the system#

Unpack the SmartBox Pro and the SiNAPS kit onto a secure surface with room for air to move. Then, in this order:

1. Plug the SmartBox Pro AC adapter into a 110–220 V outlet, and its DC output into the 9 VDC port of the SmartBox Pro.
2. Plug the SiNAPS interface box AC adapter into a 110–220 V outlet, and its DC output into the 5 VDC port of the interface box.
3. Connect the SiNAPS–SmartBox Pro HDMI cable from the interface box SMARTBOX PRO port to port A of the SmartBox Pro.
4. Connect the blue USB cable from the back of the SmartBox Pro to a USB 3.0 port on the computer.
5. Press and release the SmartBox Pro power button with the computer on and online. The computer detects new hardware — Opal Kelly XEM6310-LX45 — and installs the driver itself.
6. Connect the SiNAPS probe interface cable, with its mezzanine adapter fitted, to the ACTIVUS-SINAPS port on the interface box.
7. Optionally, run a banana cable from the SmartBox Pro ground port to a low-noise earth ground. In an electrically noisy room this is worth doing.

[!NOTE]

If the driver does not install, or Allego does not find the SmartBox Pro, install the driver from the Radiens download page ↗.

Computer requirements#

Sizing is set by throughput — channel count times sample rate — and it is specified once, in Radiens System Requirements. Read it there rather than from this page.

One thing is decided for you: every SiNAPS probe is 256 or 1,024 channels at 20 kHz, so a SiNAPS rig always sizes to the "256 channels and above" tier — never the entry tier, whichever probe you run. The dedicated GPU in that tier is not optional for SiNAPS work; the probe heat map and the 3-D model are what you read a calibration from.

Install Allego#

Installing Allego and creating a Radiens ID are the same on every rig, SiNAPS or not, and are documented in the Radiens manual: Allego → Install and sign in ↗. Get the build from the Radiens download page ↗.

Come back here once Allego launches and you are signed in — the next step is SiNAPS-specific.

Confirm the hardware#

With both boxes powered and connected, Allego finds the hardware itself.

1. Open the System tab.
2. From the Mode drop-down, select SmartBox Pro SiNAPS 256 ch or 1024 ch, to match the probe that is physically connected.

The sample rate on the System view is set to 20 kHz.

To learn the interface before a real session, select Training: Simulated spike data from the same Mode menu — Allego then simulates a 32-channel headstage on port A. Training: Sine waves simulates 64 channels across ports A and C, which is the easier one for exercising filters.

Firmware update#

You need two things from NeuroNexus before you start: the firmware file and the Opal Kelly FrontPanel tool. Ask support for both.

Reach the FPGA board#

1. Unplug the power supply from the SiNAPS interface box.
2. Remove the top and back plates to reach the small FPGA board attached to the large PCB inside. This needs a TR10 Torx bit or a similar-sized hex key.
3. Connect the blue USB cable used with the SmartBox Pro to the connector on the FPGA board, and the other end to the computer. It is a USB-A to USB Micro-B cable — contact us if you do not have one.
4. Reconnect the power supply to the interface box.

Write the firmware#

Unzip and install Opal Kelly FrontPanel, then run it. The board's model and name appear in the main window.

1. Click Program flash device — the right-most button.
2. In the Flash Programming window, set:

3. Click Start. The progress indicator reports completion after one to two minutes.
4. Close FrontPanel.
5. Power-cycle the interface box. The new firmware loads on the next power-up; without this the update is not in effect.

Calibration#

The wet test checks the electrical and electrode performance of a SiNAPS probe in saline, and sets the amplifier bias it will run at. Run it before every experiment, and run it again after insertion — the tissue changes the bias the probe needs.

Two conditions matter and both are easy to get wrong:

• Work in dark conditions. The active pixels are photosensitive, and light produces photoelectric artifacts that look like probe faults.
• Work in an electrically quiet spot, away from switching equipment.

The self-calibration is automatic. The manual adjustment described below is for the cases it does not settle.

Set up the test#

1. Cable the system as in Setup.
2. Connect the probe to the SiNAPS probe interface cable.
3. Fill a container with saline buffer — saline solution or PBS.
4. Put the probe and a reference wire into the buffer.
5. Start Allego and sign in.
6. Turn on the SmartBox Pro.
7. In the System tab, select the hardware mode — 256 or 1024 — matching the probe that is connected. (The tab itself is documented in System ↗.)

8. Open Signal Metrics beside the System tab, and click Stream. (Signal Metrics ↗ covers the module; what follows is how a SiNAPS calibration reads in it.)

Run the self-calibration#

Set these three before calibrating:

Then select Recording Mode from Signal Mode and click CALIBRATE. The run takes up to two minutes.

Read the result#

Two things tell you the probe is biased correctly.

The traces. Every channel shows a stable signal — a sawtooth, when Raw filter mode is selected. Traces are Monitor ↗; filter mode is set in Signal Processing ↗.

The heat map. The probe colour map — the Signal Metrics ↗ probe map, running live — is close to uniform. A few sites behaving differently from the rest is normal; a shank or a block of sites standing apart is not.

What saturation looks like. Vref_FFA sets the amplifier's operating point, and the raw trace shows immediately when it is wrong. Below, the same signal at a low, a correct and a high Vref_FFx: the outer two panels are saturated and flat; only the middle panel is amplifying.

That gives you the two rules the troubleshooting table repeats: signals saturated high (above ~1600 ADC) mean Vref_FFA is too low; saturated low (below ~800) mean it is too high.

Adjust Vref_FFA by hand#

Each shank has its own reference — Vref_FFA, FFB, FFC and FFD. When the self-calibration leaves one shank behind, change that shank's reference rather than re-running the whole calibration. To address dead pixels on shank 2, for example, change Vref_FFB.

A well-calibrated probe in saline sits at a uniform reference across all four shanks.

After insertion#

Vref_FFA does not stay where the wet test left it. As the electrode interface wets, the value it needs drifts, and it keeps drifting until the surface stabilises — which can take several minutes and depends on how hydrophilic the device is. Re-adjust it, by hand or by re-running the self-calibration, until it settles.

In vivo#

This is the practice around an in-vivo session — before, during and after. It assumes the probe has already passed the wet test.

Before the animal#

Surgical technique is covered in the NeuroNexus general surgery guidelines ↗ for acute and chronic experiments. Cable the system as in Setup and run the wet test before the probe goes into tissue.

Insertion#

1. Head-fix the animal on the stereotaxic frame.
2. Make either one large square craniotomy, or two small craniotomies close together.
3. Connect the probe to the system.
4. Insert the reference wire — silver or platinum, already connected to the GND pin of the probe's PCB headstage — a few millimetres into the tissue, and secure it.
5. Bring the probe tip to the insertion site.
6. Insert to the depth you want.
7. Wait 15 to 20 minutes for the electrode surface to stabilise before calibrating. Watch the traces settle in Monitor ↗ while you wait.

Calibrate in tissue#

Run the same calibration you ran in saline. Two things are different in vivo.

Read both in Signal Metrics ↗, the same module the wet test used.

Expect 600 to 900 mV. In a well-referenced animal the shank references — Vref_FFA, FFB, FFC, FFD — settle above 600 mV and below 900 mV. Values outside that range point at the reference or the ground, not at the probe.

Expect them to fall. Over the first 15 to 30 minutes after insertion, keep checking the probe and re-adjusting, by hand or by re-running the self-calibration. The references should decrease over time, as the electrode couples to the tissue and the surface wets.

If the noise floor is high, ground the animal and the surrounding equipment properly first — the systematic version of that hunt is Noise Reduction and Troubleshooting. After removing a large noise source, recalibrate: the correct bias moves with the noise.

Practices that pay#

Pre-soak the probe. Leaving the device for a few hours in a wet environment — saline, PBS, neurobasal — before insertion shortens the time the shank references take to stabilise.

Watch what saline on the brain does. Adding saline on top of the brain changes the coupling between reference and tissue, so the references the probe needs change with it. When the saline dries, they return to where they were.

Ground the stereotaxic frame. The frame itself is a common noise source. Short it to the system's analog ground — the TP8 pin — with an alligator lead.

Keep switching electronics off the animal. Thermal pads are the usual offender. Use an infrared thermal pad instead.

Rinse after use. Rinse the device in deionised or distilled water, and follow the probe care instructions for the rest.

Troubleshooting#

One table, both contexts. Where says whether a row applies during the wet test, in vivo, or both — several symptoms look identical in the two settings and have different causes.

The two saturation rows are the same rule seen from either side: too low and the signal rides above the ADC range, too high and it sits below it. Either way the raw trace goes flat, and What saturation looks like shows the three cases side by side.

Software#

Allego drives the hardware; its window, modules and account setup are documented in the Radiens manual on radiens.ai.

• Allego ↗ — the window, the module drawer, the dashboard, and creating a Radiens ID.
• System ↗ — where you select the SiNAPS hardware mode and the sample rate.
• Signal Metrics ↗ — the per-site metrics and the probe heat map calibration is read from.
• Monitor ↗ — the live traces.
• Impedance ↗ — per-site impedance as a probe map and a table, before you commit to a recording.

Probe maps#

Site numbering for the SiNAPS-1S-256, 4S-1024 and 8S-1024 probes is a separate page, with the print-scale PDFs: SiNAPS Probe Maps.

Support#

Technical questions: support@neuronexus.com · +1.734.913.8858

Check the SiNAPS product pages ↗ for the current probe range, and the Radiens download page ↗ for the current Allego build.