loopbio blog

Motif 5.0

Written on Tuesday July 02, 2019

Motif video recording software version 5.0 was released today. This version features an enormous number of new features which continue to make Motif the most capable and versatile solution for biologists looking to recording video and other data from behavioural experiments.

Windows Support

This release adds support for running the Motif software on Windows 10. The user interface and the available features are identical to when running the software on Linux.

alignment feedback

I/O, DAQ, Sensor and Output Support

Motif already allows control of IO and reading of environmental sensors from within the software, including support for the low cost phidget devices. We now support the entire phidget range.

sensor and output values are shown in the UI

a small sample of the existing supported IO devices

In Motif 5, I/O and DAQ support has improved to support more types of hardware, and control and monitoring of configured IO has been improved throughout the software. Of particular note are the following enhancements:

  • Automatic synchronization of IO/DAQ signals with video data. Values of all configured input in Motif will be stored with the recorded video (see information on our imgstore format), including both the framenumber and timestamp of the video.
  • Scheduled and manual control of configured outputs. Any changes to any defined IO/DAQ output will also be saved in the recorded data (as above, in imgstore). This ensures that not only are sensors able to be synchronized with recorded video, but any stimulus changes (scheduled or manually set using the Motif API) are too.
  • Ability to manually control configured outputs in the user interface (see screenshot). The current value of all configured inputs is also shown.
  • IO signals can be set using the Motif API. They can be changed programatically, either from experiment scripts or via the scheduler function. Expected forthcoming scheduled changes to IO are now shown in the UI (see screenshot)
  • Support for other IO types, including certain National Instrument DAQs, and control of IO over HTTP and ZMQ protocols
sensor and output values are shown in the UI

Improved IO support. Current sensor values and outputs are shown and adjustable in the UI. The value of any configured output can be changed programatically via the Motif API or scheduled to do so.

Experiment Scripts and Scripting Improvements

A major new feature is the improvement and integration of scripting and experimental scripts into the user interface. Experiment scripts are written in Python (by default, MATLAB and other scripting environments are also supported).

Users can define experimental scripts and then launch these from within Motif. Scripts are placed in a platform-specific directory. These scripts can interact with Motif using the Motif API in several ways:

  • Scripts can operate in a one-time fashion, for example by setting up an experimental protocol consisting of scheduled outputs and recordings. For more experimental scripts which use the scheduler, see the examples in the experiment script documentation
  • Scripts can also run continuously, manipulating the Motif API in realtime
  • Advanced scripts can even perform realtime image processing to implement closed loop behavioural paradigms depending on the animal behaviour

Scripts placed in the appropriate directory are then shown in the user interface, where they can be launched.

Scripts can be complicated closed loop image processing operations, collections of camera / imaging setting changes, or complete descriptions of experimental protocols including recording time and duration, metadata, stimulus, and much more. For example, the script below implements the following hypothetical experimental paradigm:

Record for 30 minutes, every-hour-on-the-hour between 6am and 4pm. While recording alternately flash a red and blue LED every second.
from motifapi import MotifApi

api = MotifApi()

camera_serial = '22075785'

# initialize LEDs
api.call('io/led_red/set', value=0)
api.call('io/led_green/set', value=1)

# schedule recording
         cron_expression='0 6-16 * * * *',

# describe stimulus protocol (flash 'inf') LEDs
api.call('schedule/camera/%s/io/led_red/set' % camera_serial,
         cron_expression='%2 * * ? * * *',
api.call('schedule/camera/%s/io/led_green/set' % camera_serial,
         cron_expression='%2 * * ? * * *',

Improved User Interface

The user-interface has been polished and unified across the various modes of Motif operation: single-camera mode, and the multiple camera 'master' and 'index' modes. Features which were previously restricted to single camera interfaces (IO and timed recording) have been added to the multicamera interface.

modes of operation

The user interface of the three main modes of Motif operation

Live Image Streaming / Closed-loop Image Processing Support

Motif 5 adds the ability to, with very low latency (<1ms), stream realtime images from the camera, without interfering with the recording, compression, or any other Motif functions. This allows realtime image processing algorithms for closed loop experiments.

Such realtime algorithms can freely use the Motif API and thus, for example, provide stimuli to the animal using configured Motif IO, or user provided custom outputs.

We unveiled this feature at Göttingen Neuroscience Conference with the demo below: A Motif system simultaneously records video and detects the position of the animal before providing a stimulus illuminating LEDs underneath (using Motif IO). Motif saves not only the video, but synchronized with it, the IO status too. From the saved data file Motif thus allows easy analysis of behaviour and stimulus after the experiment.

If you are planning to perform closed loop experiments then consider Motif, it solves all the saving, I/O, reliability, and synchronization problems for you.

Expanded Camera Range Support

This release adds support for cameras from FLIR (formerly Point Grey), extends our support for Basler cameras, adds support for network cameras and standard operating system supported cameras (v4l on Linux and UVC on Windows).

alignment feedback

A small sampling of the more than 300 supported cameras.

Extended Trigger and Synchronization Options

Motif 5 added support for a number of different trigger and synchronization scenarios commonly necessary when synchronizing video recording with neurophysiology recording or stimulation setups. This allows Motif to either take a variety of 'master' or 'slave' roles with respect to the the triggering and recording of frames. Motif can consume trigger pulses produced by other hardware, or generate a variety of different trigger pulses for recording by the secondary neurophysiology hardware.

If you need video synchronized with neurophysiology, electrophysiology, or other hardware devices then contact us to see what Motif can do for you.

Complete and Comprehensive Documentation

Comprehensive documentation is provided online and is continually updated. Documentation explains the use and confiugraton of Motif, as well as use of the Motif API and example experiment scripts.

motif documentation

Interested in Motif?

Motif is the first video and camera recording system designed for the experiments of modern scientists. It supports single and multiple synchronized camera scenarios, remote operation, high framerate and unlimited duration recording. It is always updated and has no single-user or other usage limitations.

If you are interested in a Motif system, please contact us for a quote or to see how Motif can solve your video recording needs.

New Open Source Releases: Imgstore and Stitchup

Written on Monday February 25, 2019

Over the last couple of months we released a couple of interesting open source tools that might be of use to some hackers out there. In typical bad-at-marketing-busy-company form we then forgot to blog about them!

Stitchup is a python library for stitching multiple videos together into a larger video mosaic or video panorama. This is a common scenario for users of Motif video recording systems who have multiple-camera setups to increase their spatial and temporal resolution.


Stitchup adds some functionality (storing and loading of calibrations) and considerably improves upon the OpenCV in-tree stitcher module Python API. Stitchup was used in the example above and for our previous post on multi-camera high throughput c.elegans screening assay

Imgstore is a seekable and scalable for video frames and metadata (see announcement and imgstore introduction here). Well, we just released version 2.0 (and then 2.1, 2.2, and 2.3).

API compatibility was retained, however the 2.0 release features a few nice new features and signifigant bugfixes

The new version can be installed from pypi using pip install -U imgstore.

Interested in Motif?

Motif is the first video and camera recording system designed for the experiments of modern scientists. It supports single and multiple synchronized camera scenarios, remote operation, high framerate and unlimited duration recording. It is always updated and has no single-user or other usage limitations.

If you are interested in aMotif system, please contact us for a quote or to see how Motif can solve your video recording needs.

2018 In Review

Written on Monday January 07, 2019

2018 was a great year for loopbio! We continued to improve our products, particularly Loopy image processing and tracking software, and Motif video recording software, and our Virtual Reality systems, to meet the needs of quantitative biologists around the world.

We are especially happy with the improvements and success of Loopy, which left beta testing in January 2018 and grew in popularity rapidly - over the course of 2018 Loopy was used:

  • To help 149 scientists with their research
  • To process 10577 videos (totalling 14.9TB of data)
  • To track or analyze, using deep learning, 2D or 3D tracking, 3484 videos
  • To annotate 2368 video segments
  • To score 791 experiments

Let's review the year in order and highlight some of the moments we are most proud of, including:

Loopy Is Born

At the turn of the year we launched Loopy to the general public, making deep learning and 3D tracking available to all scientists immediately, without having to write or maintain their own software. Loopy can be used immediately by signing up at https://app.loopb.io.

Loopy Grows Up

After Loopy's release, we didn't' stop adding features. We began by added scoring and behavioral coding to Loopy, including social scoring.

We taught all our products - Loopy, Motif, and realtime 3D tracking to get along with one another, demonstrating a world first at FENS conference: realtime marker free pose tracking of mice (and other animals).

We added even more plotting and data analysis capabilities to Loopy - making it a complete and integrated tool for analysis. Now you can create your own tracking solution, including training your own deep learning based detector animal tracker, upload and process videos, and plot and analyze data, without leaving your web browser.

We polished our complete suite of tools for 3D tracking, calibration and analysis. Use your deep learning animal or pose detector for 3D reconstruction with ease!

Motif - the Versatile Video Recording Platform

2018 featured a number of cool uses and examples of Motif - our recording software which can be used standalone, or combined across multiple computers to build complex and automated experimental assays.

Here's Motif for longterm activity recording.

Motif for microscope-like resolution and high framerate recording from multi-well plates.

Motif for wide-area high framerate recording with realtime compression.

Motif for synchronized multi-camera 3D recording - collecting data for analysis in Loopy.

Virtual Reality

We developed and delivered an innovative virtual reality system for flies.

We also delivered two FishVR systems to customers.

2018 was a great year for loopbio!
We wish everyone a happy new year and look forward to 2019!

A Multi-Camera High Throughput Worm Assay

Written on Wednesday October 17, 2018

We were approached by Andre Brown to create a custom imaging setup for high-throughput worm screening. Dr. Brown and his team are searching for novel neuroactive compounds using the nematode C. elegans. He explained:

"To screen a large number of drugs, it helps to image many worms in multiwell plates. Normal plate scanning microscopes don't help because we want to see behaviour changes that require looking at each worm for minutes so we have to image the worms in parallel. At the same time, we need enough resolution to extract a detailed behavioural fingerprint using Tierpsy Tracker. A six-camera array provides the pixel density and frame rate we need and opens the door to phenotypic screens for complex behaviours at an unprecedented scale."

The Solution

To meet the requirements we designed a solution using 6x 12 Megapixel cameras at 25 frames per second. To save on storage space, all video is compressed in real-time, at exceptional quality, before being saved to disk. The flexibility of Motif allows synchronized recording from all cameras, controlled from a single web-based user interface.

For an impression of the images possible with such a system, check out the interactive (mouse over / touch for zoom controls) viewer below.

unfortunately the generation of the visualisation above introducted some artifacts not present in the orignal video

Interested in Motif?

Motif is the first video and camera recording system designed for the experiments of modern scientists. It supports single and multiple synchronized camera scenarios, remote operation, high framerate and unlimited duration recording. It is always updated and has no single-user or other usage limitations.

If you are interested in a Motif system, please contact us for a quote or to see how Motif can solve your video recording needs.

Loopbio Joins NVIDIA Inception Program

Written on Thursday October 04, 2018

We are happy to announce that loopbio gmbh has been accepted into the NVIDIA Inception Program. The program is designed to nurture dedicated and exceptional startups who are revolutionizing industries with AI and data science. The Inception Program provides direct access to NVIDIA's latest technology, deep learning expertise, and a global network of partners and customers.

Loopbio was the first company to bring easy to use deep learning based video analysis and tracking soulutions to the quantitative and behavioural biology research fields. Our revolutionary loopy product was launched in 2017 and allowed AI tracking and analysis of animal behaviour, using only your web browser and without writing any code. Loopy has been improved ever since with the addition of state of the art AI algorithms for pose and 3D tracking, and image and behavioural classification.


Unlike other AI platforms, loopy does not stop at just model training. It provides comprehensive tools for performing quantitative analysis on processed video to let users get high quality scientific data faster.

About Loopbio

Loopbio was founded in 2016 to bring cutting edge technology to behavioural biology. The company is based in Vienna and provides integrated solutions for high-speed single- and multiple-camera video recording, video analysis and tracking, and virtual reality.

Motif Version 4.5 - New Features

Written on Tuesday August 28, 2018

Following the last release we have continued to add features and improvements to our Motif software. This post includes a short overview of some hightlights, while a full list of changes is provided on our website.

Each and every Motif system receives automatic updates without any extra charge.

Increased Support for Environmental Sensors

We have improved our support for environmental sensors from Phidgets greatly. This means that you can simply connect any one of their 'VINT' series sensors to a Motif system and you can now take sensor recordings automatically, at several different sample rates. Phidgets offer an enormous variety of sensors which can be used to measure various parameters of your experiment while recording video, including;

compatible sensors

A selection of compatible sensors

Because we record to our extensible and open imgstore format, all sensor recordings are immediately associated with both the time and framenumber of the video being recorded.

Controlling Outputs

In addition to measuring environmental sensors, we added the ability to switch on or off supported Phidgets outputs, relays and motors. Using our open API you can now, for example, perform tasks like the following

  • control experimental stimuli at regular or scheduled times
  • control physical devices such as motors, servos or actuators
  • switch on/off LEDs, lights or other stimuli
  • schedule tasks for before or after recording has been completed, such as automated feeding or cleaning procedures

Improved Integration with Loopy

Following on from above, if you have a recording with environmental data associated, this will be immediately visible in Loopy after the imgstore has been uploading or imported.

environmental readings showing in loopy

Graphing and export of environmental data associated with a recording is displayed in Loopy

Automatic Import

If you are running an on-site version of Loopy, your Motif and Loopy systems can be configured to allow automatic import of recordings after the completion of your experiment. This feature is especially advantageous when both systems are integrated with your IT infrastructure because all video and experimental data is automatically added to your shared and backed-up network storage without risk of deletion or loss.

loopy integration

Simply enter you Loopy username and your recording will be automatically backed up and imported

Further descriptions of the powerful integrations between Motif and Loopy will be the subject of a future blog post.

New Alignment Visualization

The last motif release added a number of image feedback augmentations to help with setting up your cameras and experimental assays. This release added a new visualization designed to help with alignment of samples inside the experimental apparatus, or to help align multiple cameras in a multiple-camera situation.

alignment feedback

The center of the image is indicated, in addition to concentric bands respecting the aspect ration of the camera sensor.

Interested in Motif?

Motif is the first video and camera recording system designed for the experiments of modern scientists. It supports single and multiple synchronized camera scenarios, remote operation, high framerate and unlimited duration recording. It is always updated and has no single-user or other usage limitations.

If you are interested in a Motif system, please contact us for a quote or to see how Motif can solve your video recording needs.