Recording Configuration
To record from a probe, you will need to specify the recording configuration using a synapse JSON file. A configuration file specifies the nodes in the signal chain, as well as how they are connected. An example configuration file for the Axon Omnetics adapter is provided below that defines which channels are being recorded from, the bit depth and sample rate of the recording, and the high- and low-pass filter corner frequencies. Please refer to the Synapse peripheral documentation for a complete list of configuration options.
{
"nodes": [
{
"type": "kStreamOut",
"id": 1,
"stream_out": {
}
},
{
"type": "kBroadbandSource",
"id": 2,
"broadband_source": {
"peripheral_id": 100,
"sample_rate_hz": 32000,
"bit_width": 12,
"signal": {
"electrode": {
"channels": [{"id": 0, "electrode_id": 122, "reference_id": 520}, {"id": 1, "electrode_id": 126, "reference_id": 520}, {"id": 2, "electrode_id": 116, "reference_id": 520}, {"id": 3, "electrode_id": 120, "reference_id": 520}, {"id": 4, "electrode_id": 110, "reference_id": 520}, {"id": 5, "electrode_id": 114, "reference_id": 520}, {"id": 6, "electrode_id": 104, "reference_id": 520}, {"id": 7, "electrode_id": 108, "reference_id": 520}, {"id": 8, "electrode_id": 98, "reference_id": 520}, {"id": 9, "electrode_id": 66, "reference_id": 520}, {"id": 10, "electrode_id": 92, "reference_id": 520}, {"id": 11, "electrode_id": 60, "reference_id": 520}, {"id": 12, "electrode_id": 86, "reference_id": 520}, {"id": 13, "electrode_id": 54, "reference_id": 520}, {"id": 14, "electrode_id": 80, "reference_id": 520}, {"id": 15, "electrode_id": 48, "reference_id": 520}, {"id": 16, "electrode_id": 74, "reference_id": 520}, {"id": 17, "electrode_id": 38, "reference_id": 520}, {"id": 18, "electrode_id": 68, "reference_id": 520}, {"id": 19, "electrode_id": 36, "reference_id": 520}, {"id": 20, "electrode_id": 62, "reference_id": 520}, {"id": 21, "electrode_id": 0, "reference_id": 520}, {"id": 22, "electrode_id": 56, "reference_id": 520}, {"id": 23, "electrode_id": 4, "reference_id": 520}, {"id": 24, "electrode_id": 50, "reference_id": 520}, {"id": 25, "electrode_id": 12, "reference_id": 520}, {"id": 26, "electrode_id": 44, "reference_id": 520}, {"id": 27, "electrode_id": 14, "reference_id": 520}, {"id": 28, "electrode_id": 42, "reference_id": 520}, {"id": 29, "electrode_id": 20, "reference_id": 520}, {"id": 30, "electrode_id": 32, "reference_id": 520}, {"id": 31, "electrode_id": 26, "reference_id": 520}],
"low_cutoff_hz": 4,
"high_cutoff_hz": 20400
}
}
}
}
],
"connections": [
{
"src_node_id": 2,
"dst_node_id": 1
}
]
}
Synapse API
Recordings with SciFi is initiated using synapsectl. The --help command outputs a list of all available commands.
$ synapsectl --help
usage: synapsectl [-h] [--uri URI] [--version] [--verbose]
{discover,info,query,start,stop,configure,logs,read,plot,file,taps,deploy,build} ...
Synapse Device Manager
options:
-h, --help show this help message and exit
--uri URI, -u URI The device identifier to connect to. Can either be the IP address or name
--version show program's version number and exit
--verbose, -v Enable verbose output
Commands:
{discover,info,query,start,stop,configure,logs,read,plot,file,taps,deploy,build}
discover Discover Synapse devices on the network
info Get device information
query Execute a query on the device
start Start the device or an application
stop Stop the device or an application
configure Write a configuration to the device
logs Get logs from the device
read Read from a device's StreamOut node
plot Plot recorded synapse data
file File commands
taps Interact with taps on the network
deploy Deploy an application to a Synapse device
build Cross-compile and package an application into a .deb without deploying
Synapse Apps
Synapse Apps are standalone applications that can be deployed to a synapse device, such as SciFi. Apps allow you to run your own custom neural processing algorithms on device to minimize latency. Apps read in data from other nodes in the signal chain, and Taps are used to output data to a local client running synapsectl.
Configuration files can be uploaded to the Synapse device while starting a Synapse App.
synapsectl -u "device uri" start <path to config>.json
For more information about writing and using apps running on your Synapse-compatible headstage, see the App API.
Measure Impedance
Query Construction
In order to request an impedance measurement from a Synapse device, you will need to construct and format an “Impedance Query” message to send to the SciFi in the form of a JSON file:
{
"query_type": "kImpedance",
"impedance_query": {
"electrode_ids": [1, 2, 3, 4, 5]
}
}
Your list of electrode IDs can be as long as you’d like.
Run the Test
Use the following command to begin the measurement:
synapsectl -u $DEVICE_IP query $QUERY_JSON_PATH
The command may take a few minutes if your list of electrode IDs is large.
After the measurement finishes, an output is generated with a status message (typically blank) and a list of each electrode measurement measured by magnitude (Ohms) and phase (degrees). The output file is saved in a CSV format and titled impedance_measurements_$DATE_$TIMESTAMP.csv.
status {
}
impedance_response {
measurements {
electrode_id: 1
magnitude: 13414576.0
phase: -210.17554
}
measurements {
electrode_id: 2
magnitude: 28159914.0
phase: -184.9782
}
measurements {
electrode_id: 3
magnitude: 12796945.0
phase: -168.97946
}
measurements {
electrode_id: 4
magnitude: 31529048.0
phase: -248.70753
}
measurements {
electrode_id: 5
magnitude: 1768543.4
phase: -147.09204
}
}