loopbio blog

2018 In Review

Written on Montag Jänner 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!

Loopbio Joins NVIDIA Inception Program

Written on Donnerstag Oktober 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.

conda

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 Dienstag 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?

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.

2018 Conferences

Written on Freitag März 23, 2018

Conference season is here! If you are interested in seeing our products or talking to us in person about your scientific needs you can meet us at the following places.

This post will be updated as we confirm or add more dates.

loopbio supports conferences at the beach

Motif 4.0

Written on Montag November 27, 2017

Motif video recording software version 4.0 was released today. This version features many changes and improvements, as demonstrated in the following youtube video


Motif is a video recording sytem which supports single single camera or multiple camera recording, and video recordings can be from seconds to weeks in duration. The version 4.0 release has the following highlights:

Motif 4.0 screenshots

Sample screenshots of Motif 4.0 multi-camera and single-camera web user interface

I'd like to demonstrate a the last two of these features using the new Python API.

Starting and stopping recording is easy. The following snippet demonstrates starting recording on all cameras with the predefined compression settings named 'high' (see the Web UI for the names of your configured compression formats). The recording will run for 5 seconds and will have have the additional metadata 'experiment' and 'genotype' saved to the recorded file. The snipped works equally on single or simultaenous multiple-camera systems.

from motifapi import MotifApi

IP_ADDRESS = '10.11.12.13'
API_KEY = 'abcdef123456abcdef123456abcdef12'
api = MotifApi(IP_ADDRESS, API_KEY)

api.call('recording/start',
         codec='high',
         duration=5,
         metadata={'experiment': 'frobnicate', 'genotype': 'wt'})

Likewise, the API also supports defining scheduled tasks, this allows for example, to schedule recordings and their subsequent copy to storage to occur at specific times. Task scheduling re-uses Cron syntax with some extensions (monotonic tasks).

api.call('schedule/recording/start', task_name='record_video',
         cron_expression='0 06-16 * * *',
         codec='low', duration=30*60)

We are really excited about these new API feature as they allowa laboratory wide automation of single or multiple recording systems or experimental assays. We are looking forward to extending our API support in future releases.