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IO and DAQ Support

Motif can control hardware outputs (such as flashing LEDs, triggering of optogenetics hardware) and the reading of sensor data (such as temperature sensors, light sensors, pressure sensors, etc), all within the recording software.

While recording, Motif then saves the values of any outputs and sensors beside the video in a format that allows measurements to be precisely aligned with which frame number and frame timestamp they occurred.

Note

Motif's built in IO support is designed for relatively low sample rates of ≤100Hz. If you need a higher sampling rate then please contact support@loopbio.com

IO Outputs can be controlled via the REST API, from experiment scripts, and can be configured to appear in the WebUI.

A small example of some of the supported sensors and outputs from the Phidgets IO backend

Controlling IO From the WebUI

The "I/O & Scheduled" tab provides a simple way to see the state of any configured outputs and sensors.

Note

The WebUI only updates the value of configured sensors at 2Hz, which means if you have configured a fast sample rate, the values here will update much slower. However, the full data will be present in the data file.

Info

The screenshot above shows the result of the example script here scheduling the flashing of the two configured LEDs (red and green). The corresponding configuration for this is here

Supported IO Types

Motif supports a number of different backends - however once configured, all backends are conceptually alike. Motif takes care of integrating the IO values with the recording to make combining the data easy.

Note

Integration and configuration of an IO backend is an advanced task. Please contact support@loopbio.com for advice and help.

  • Phidgets
    Phidgets are low-cost sensors and controllers which are the easiest way to add support for controlling outputs (e.g. LEDs or other electro-mechanical devices like motors, or servos). Motif supports all Phidgets devices including the following extensive list of sensors (see here).
    • Temperature/Humidity
    • Distance
    • Light/Sound
    • Motion
    • Voltage/Current
    • Load Cells
    • FSR
    • Proximity
    • Touch / Human Input
    • Gas Pressure
    • Rotary Position
    • Linear Position
    • Adapters
    • pH/ORP
  • HTTP
    The HTTP backend allows Motif to integrate sensors that expose their information over a HTTP GET (json) endpoint, or outputs that can be controlled using HTTP POST (json) requests.
  • ZMQ (advanced use)
    The ZQM backend allows you to integrate an out of process measurement or control system of your own design, and providing you expose those values over ZMQ in the correct manner, Motif will take care of including them in the resulting data file.
  • National Instruments DAQ Devices (Windows only)
    On Windows Motif can integrate with NI DAQs and record data a very high sampling rates. This module is additional to the normal Motif package, please contact support@loopbio.com

Example: Phidgets LEDs and Temperature Sensor

The following example configuration file snippet (i.e. not the whole file) configures the IO backend as can be seen in the screenshot above

IO:
  Backend: phidgets
  Outputs:
  - name: led_red
    device_type: 'DigitalOutput'
    port: 0
  - name: led_green
    device_type: 'DigitalOutput'
    port: 1
  Sensors:
  - name: temperature
    device_type: '1124'
    port: 2
    fs: 1
  UI:
    Outputs:
    - default_val: 0
      label: Red LED
      max_val: 1
      min_val: 0
      step: 1
      name: led_red
    - default_val: 0
      label: Green LED
      max_val: 1
      min_val: 0
      step: 0.1
      name: led_green
    Sensors:
    - {name: 'temperature'}

IO Format

The default format for saving IO values is json. If the current recording is an [imgstore] (see: recording to an imgstore), then the IO data is stored inside the imgstore directory. The data can then be loaded using the imgstore API.

If the current recording is to a single file, then the extra data is saved to a json file with the same name, but with .extra_data.json appended.

In both cases the .extra_data.json files contain a list of json records. For the example above, a snippet from an extra data file contains;

[{"frame_index": 8314, "frame_time": 1559671159.517081, "sensor_time": 1559671159.54632, "is_recording": true, "recording_sequence_number": 2, "recording_start": 1559670882.357428, "frame_number": 3554885, "temperature": 27.26},
{"led_red": 0, "recording_sequence_number": 2, "frame_index": 8328, "is_recording": true, "frame_time": 1559671159.983759, "frame_number": 3554899, "recording_start": 1559670882.357428},
{"recording_sequence_number": 2, "frame_index": 8328, "is_recording": true, "led_green": 1, "frame_time": 1559671159.983759, "frame_number": 3554899, "recording_start": 1559670882.357428},
{"frame_index": 8344, "frame_time": 1559671160.517131, "sensor_time": 1559671160.545529, "is_recording": true, "recording_sequence_number": 2, "recording_start": 1559670882.357428, "frame_number": 3554915, "temperature": 27.26}]

(many values omitted)

Note the presence of the following values in every row:

  • frame_index
    the current frame number of this recording
  • frame_number
    the current frame number of the camera (since synchronization or power on, consistent across multiple cameras in a multiple camera synchronized Motif system)
  • frame_time
    unix timestamp of current frame
  • is_recording
    true if camera is currently recording
  • recording_start
    unique identifier of this recording

Additionally:

  • rows with configured sensors (e.g. temperature are omitted at the configured sample rate
  • rows with the value of any output (e.g. led_red, led_green) are written any time an output changes