• Video analysis tool to investigate zebrafish embryo and larva parameters.


If you are interested in a scope of zebrafish embryo and larvae parameters such as embryo activity, cardiovascular measurements, morphology, and gut and blood flow, then DanioScope is just what you need. This software tool uses video files and images, and it offers an easy-to-use and non-invasive way to study your zebrafish.


Most importantly, DanioScope allows you to test many animals simultaneously. This increases the throughput of your research significantly, and ultimately saves you a lot of time when it comes to preparing your experiment, acquiring data, and analyzing the results.

DanioScope is the video-based software tool for the non-invasive study of zebrafish embryo and larvae

Zebrafish embryo activity

Zebrafish develop quickly: within a matter of hours internal organs start to show. Also, movements such as tail flicks, coilings, and convulsive behavior start as early as 17 hours after fertilization. These behaviors are of interest especially in toxicological studies and pharmacology, as they reflect the development of the nervous system. Additionally, these readouts are highly susceptible to pharmacological manipulation.

DanioScope non-invasively measures these behaviors – simply use a video of one or more zebrafish embryos. DanioScope automatically recognizes each embryo (within their chorion). Then it measures their activity. If floating occurs you can simply adjust the location of the measurements during the experiment. DanioScope reports back the following parameters:

  • Burst activity – percentage of time (from total measurement duration) the embryo was moving
  • Inactivity – percentage of time of inactivity (100% - burst activity).
  • Burst duration – total time spent active (sum of all movement durations)
  • Inactivity duration – total time spent inactive
  • Burst count – number of times the embryo moved
  • Burst count / per minute – number of movements per minute

Compared to manually counting activity bursts, DanioScope can save you 75% experiment time (based on beta testing by Dr. J.P. Cambero at Instituto de Salud Carlos III, Madrid, Spain. www.isciii.es).

Danioscope activity illustration
DanioScope detects zebrafish embryo activity such as tail coils or convulsions.
Danioscope activity detection
It works in a fast and easy way because DanioScope recognizes the embryos and can analyze videos with multiple animals simultaneously.

Cardiology measurements in zebrafish larvae

The heart is the first organ to develop in zebrafish, and development is similar to the human heart, both good reasons for zebrafish to be an interesting model in cardiology research.

The zebrafish cardiac system is assessed by measuring the heart rate or inter-beat interval. Traditional methods include manual counting (using a stopwatch), using a micro pressure system, Laser Doppler microscopy, or electrocardiograms. These methods are labor-intensive, time-consuming, and require specific training to perform.

Video based assessment of heart rate and inter-beat intervals is far less labor intensive. After indicating the heart area in the video imported in DanioScope, it automatically calculates the number of beats per second (BPS) and beats per minute (BPM).

This method can save you up to half the time compared to manual methods (based on beta testing by Dr. J.P. Cambero at Instituto de Salud Carlos III, Madrid, Spain. www.isciii.es).

Danioscope cardiology illustration
DanioScope measures activity in the heart of each larvae.
Danioscope cardiology graph
From this activity, the heartbeat in beats per second or per minute is extracted.

Blood (and gut) flow

Heart malfunctions might not always be evident in heart rate data. In that case, blood flow measurements are a valuable addition to a study.

Blood flow can be measured using hand counting methods that often require labor-intensive and time-consuming fluorescence labeling techniques. DanioScope uses video analysis to measure the flow in a blood vessel. In addition, it can measure gut flow in a similar fashion.

To measure flow, you select (a part of) the blood vessel or the part of the gut, from wall to wall, in your video image. Changes in pixels on a frame-by-frame basis is used to measure flow. The blood or gut flow is presented as a activity percentage.

Danioscope flow illustration
Flow activity can be measured in both blood vessels and the gut.

Morphology measurements

Besides dynamic measurements, DanioScope also allows you to easily monitor the morphology of your zebrafish. You can upload images or take snapshots from videos to monitor changes in morphology.

With intuitive drawing tools you can define distances or areas you are interested in, and after calibration DanioScope will measure lengths and surfaces automatically. This way you can easily determine tail length, eye size, and pericardial area. Or any other measurement, because you can define your own!

By images from different time point, you can easily monitor growth and malformations over time.

Danioscope morphology illustration
Intuitive tools allow you to use images or stills from your video file to measure morphological parameters such as body length and eye size.


After data acquisition, DanioScope offers options for data selection, visualization, and analysis. You can also easily export raw data for further analysis in your statistical program of choice.

DanioScope is suited to support high-speed videos (over 60 fps), and can handle a wide range of video formats.

DanioScope activity thresholds
DanioScope allows you to fine-tune the activity thresholds.


We offer DanioScope in combination with the ZEISS SteREO Discovery.V8 microscope to acquire crisp and detailed images and video files.

ZEISS SteREO Discovery.V8
DanioScope software is available in combination with the ZEISS SteREO Discovery.V8 microscope.

You can find recent publications on the DanioScope reference page.