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Configuration Guide

Motif is optimized for regular and consistent use in an experimental setting. This means that most configuration options are not accessible from the user interface (so they can not accidentally be changed between experiments) and are instead stored in the configuration file(s).

Note

Motif is supported software. If you have any difficulties configuring it, or would prefer we assist with configuration, please contact support@loopbio.com

There are three configuration files, in per-platform specific locations. The main configuration file you need to worry about, on Linux, is /etc/recnode.yml. On Windows this file is located at C:\ProgramData\Motif\recnode.yml.

In the multiple-camera case, in addition to /etc/recnode.yml, two other configuration files are (optional, can be) used to further change the appearance of only the web user interface of the individual cameras.

When the multiple-camera interface starts other cameras it parses the following files in the following order (using the Linux configuration file paths for example)

  1. /etc/recnode.yml
  2. /etc/recnode.multicam.yml
  3. /etc/recnode.CAMERA_SERIAL_NUMBER.yml

Thus later files replace earlier files. This means that you can overwrite the 'default' /etc/recnode.yml configuration for all cameras, or per camera, by putting changed settings in the other configuration files. For example, you might want to disable control of individual camera UI elements using the various EnableXXX configuration options in a multiple-camera setup by adding / replacing these configuration values to only the per-camera configuration files.

Configuration Files and Syntax

The configuration files are YAML format.

  • The Configuration file is explained here
  • An example configuration file (un-annotated) is here
  • Advanced configuration tips and tricks are collected here

Tip

Motif needs to be restarted to detect configuration changes. If your Motif system is linux based, you can restart the entire Motif software without having to restart the computer by executing the command $ sudo systemctl restart supervisor.service

Synchronized and Multiple Camera Configuration

The settings in Multicam configuration mostly concern the triggerbox

  • TriggerDevice - /dev/ttyUSB0 for example
  • StartRecordingDIO - start recording upon change of this digital input
  • SynchronizeOnRecordStart - if true, automatically synchronize cameras before starting recording. This guarentees that stores start at frame_number 0.
  • AllowManualSynchronization - show a 'Synchronize Cameras` button and allow users to manually synchronize and thus reset camera frame_number=0. Note: you can only synchronize once per recording, so that only one frame_number=0 is present in a store.

Note

This section applies only to versions of Motif 5.2 or newer

When configuring a synchronized multiple camera Motif system there are a number of small differences in how individual cameras should be configured. Beginning with camera configuration, please note the following

  • Camera Configuration
  • set AcquisitionFrame to null
  • If you are using a loopbio provided triggerbox set MotifMulticamFrameRate to the desired framerate in /etc/recnode.yml
  • If you are using Basler cameras synchronized over PTP set MotifPTPFrameRate to the desired framerate in /etc/recnode.yml
  • If you are using hardware synchronized cameras but are providing the trigger signal externally, you can set MotifMulticamFrameRate to your external framerate if you wish to receive warning, for example, when an impossible exposure time is selected

Depending on the combination of trigger backend and camera type, you might need to adjust some multicam specific settings

  • If using FLIR cameras with the trigger signals on Line0 (Camera: TriggerSource: 'Line0') and a loopbio triggerbox, then you should also set `'CameraTriggerSource': 'Line0' in Multicam / Trigger / Backend Conf
  • If using the baslerptp trigger backend, cameras are detected to be 'synchronized' when their PTP timestamps are in agreement to a certain precision
  • The serial numbers of all cameras to be PTP synchronized must be listed in the Multicam setting CameraSerials
  • To change the required precision of time agreement, you can adjust the Multicam / Trigger / Backend Conf setting MaxOffsetFromMaster (it is in nanoseconds and defaults to 100)

Automatically Connecting Cameras

It is possible that in multicamera setups, Motif can automatically connect 'start' cameras as they are detected / plugged in. To enable this feature, set the Multicam setting AutoStartCameras: true. To restrict this behaviour to certain cameras only, you can enter their serial numbers in CameraSerials