Install the Headstage GUI

The Synapse Headstage GUI is a desktop client for discovering, configuring, and operating Synapse devices. It runs on Windows 10+, macOS Ventura (13.0)+, and Ubuntu 20.04 LTS+.

Connect Your Device

The homepage of the Synapse Headstage GUI will display all autodiscovered devices on your network, or you can add a device manually using the + option.

Configure and Start a Signal Chain

Signal chains define how data is processed on a device. This walkthrough uses generated simulated broadband data from the SciFi Virtual Recording Peripheral. If you want to use a physical peripheral, you will need to connect it to your device using a USB-C cable.

1. Add a Broadband Source node in the device editor and select SciFi Virtual Recording Peripheral in the first drop down.
2. Select the ↓ update button to send your signal chain to your device. A signal chain is necessary for data acquisition.
3. Select ▸ start.

Record Data from a Tap

While your device is running, you can listen to the Tap corresponding to the Broadband Source node in your signal chain.

1. Select Taps, then the Broadband Source node to see a livestream of your data.
2. To save the stream in the Synapse HDF5 format, select Record, choose a location and file name, and begin recording. Select Record again when you are ready to stop.

Write to Disk

You can also save data directly to your SciFi.

1. Return to the Editor tab and stop your signal chain.
2. Add a Disk Writer node, and connect it to the output of the Broadband Source node.
3. Update and start your new signal chain on your device and it will now write the broadband data to your device's onboard storage.

Access Files

You can transfer files from your SciFi to your computer using a wireless or wired connection, but we recommend a wired connection for fastest transfer times.

1. Connect your computer to the port closest to the GPIO connector using a USB-C cable.
2. Open the Files tab in the GUI.
3. Enter your SciFi's Disk Writer password, you can find it on your device under Settings > Device Info > DiskWriter Pass.
4. Select your recording, and download it to your computer.

Filter Data

You can configure your SciFi to filter data using a Spectral Filter node.

1. Return to the Editor tab and stop your signal chain.
2. Add a Spectral Filter node and another Disk Writer node and connect them in series to the Broadband Source node.
3. Adjust the filter parameters and give your second Disk Writer node a unique file name.
4. Update and start your new signal chain on your device and it will now write unfiltered and filtered broadband data to your device's onboard storage simultaneously.

Install the Synapse CLI

synapsectl is the command line client for building, deploying, and monitoring Synapse devices. Before you begin, make sure you have Python 3 and pip installed. You will also need Docker to package and deploy Synapse Apps on your device, but this is outside the scope of this guide.

Mac, Linux, and Windows are supported. WSL does not currently support all Synapse features.

We recommend a virtual environment:

# create a Python virtual environment called myenv
python -m venv myenv

# activate your virtual environment
source myenv/bin/activate

# install Synapse in your virtual environment
pip install science-synapse

Confirm the install and list the available commands:

synapsectl --help

Linux UDP Buffer

On Linux, increase the UDP buffer size. To change it immediately:

sudo sysctl -w net.core.rmem_max=10485760 # 10 MB
sudo sysctl -w net.core.wmem_max=10485760 # 10 MB

To make the change persistent, add the following file and reboot:

sudo touch /etc/sysctl.d/50-udp-buffersize.conf
# And add these lines:
net.core.rmem_max=10485760
net.core.wmem_max=10485760

macOS UDP Buffer

To change the buffer size immediately:

sudo sysctl -w kern.ipc.maxsockbuf=10485760

Or add the following to /etc/sysctl.conf:

kern.ipc.maxsockbuf=10485760

Verify Your Device

Connect your computer to the same network as SciFi 2, then run the following command to confirm the device is reachable. Replace $DEVICE_IP with the address from the device's Network tab.

synapsectl -u $DEVICE_IP info

The device reports its name, serial number, firmware version, status, and available peripherals:

   Name: walrus
   Status: Stopped
   Serial: SF2100001
   Synapse Version: v2.4.1
   Firmware Version: 8a0b6641
   Battery: 85.0%
   Storage Devices
   └── No storage devices found
   Peripherals
   ├── SciFi Virtual Recording Peripheral (Science Corporation)
   │   ├── ID: 100
   │   └── Type: kBroadbandSource
   └── VirtualOpticalStimPeripheral (Science Corporation)
      ├── ID: 101
      └── Type: kOpticalStimulation

If the command times out, your computer and SciFi 2 may be on a network that blocks device-to-device traffic. See the FAQ for troubleshooting.

Configure a Signal Chain

A signal chain defines how data moves through the device, and is sent to the device as a JSON configuration.

Use the following example configuration which ingests data from six electrodes, filters it through a bandpass filter, then writes the filtered data to the onboard device storage.

{
  "nodes": [
    {
      "type": "kBroadbandSource",
      "id": 1,
      "broadband_source": {
        "peripheral_id": 100,
        "bit_width": 12,
        "sample_rate_hz": 32000,
        "gain": 0,
        "signal": {
          "electrode": {
            "channels": [
              { "id": 0, "electrode_id": 0, "reference_id": 512 },
              { "id": 2, "electrode_id": 2, "reference_id": 512 },
              { "id": 4, "electrode_id": 4, "reference_id": 512 },
              { "id": 250, "electrode_id": 250, "reference_id": 515 },
              { "id": 252, "electrode_id": 252, "reference_id": 515 },
              { "id": 254, "electrode_id": 254, "reference_id": 515 }
            ],
            "low_cutoff_hz": 57,
            "high_cutoff_hz": 13489
          }
        }
      }
    },
    {
      "type": "kSpectralFilter",
      "id": 3,
      "spectral_filter": {
        "method": "kBandPass",
        "low_cutoff_hz": 92,
        "high_cutoff_hz": 4365
      }
    },
    {
      "type": "kDiskWriter",
      "id": 2,
      "disk_writer": {
        "filename": "scifi-test",
        "storage_device_id": 1
      }
    }
  ],
  "connections": [
    { "src_node_id": 1, "dst_node_id": 3 },
    { "src_node_id": 3, "dst_node_id": 2 }
  ]
}

Send the configuration and start the device:

# send your configuration
synapsectl -u $DEVICE_IP configure $PATH_TO_CONFIG.json

# start the device
synapsectl -u $DEVICE_IP start

Stream a Tap

Read from the Broadband Tap and save the stream to your computer as HDF5:

synapsectl -u $DEVICE_IP read --output $OUTPUT_PATH

Stop the device when you are finished:

synapsectl -u $DEVICE_IP stop

Download a Recording

List the device's own storage and retrieve it:

synapsectl -u $DEVICE_IP file ls disk_writer/
synapsectl -u $DEVICE_IP file get -r disk_writer/scifi-test

The first time you access files on your device, you will be prompted for its Disk Writer password. You can find it on your device's display under Settings > Device Info > DiskWriter Pass.