DanioScope

DanioScope is a software system developed by Noldus for measuring physiological and behavioral parameters in zebrafish embryos and larvae. It is designed for researchers working in areas such as toxicology, pharmacology, and cardiology who need to assess embryo activity, cardiovascular function, blood and gut flow, and morphological changes. The system supports testing multiple animals simultaneously, which increases experimental throughput and reduces the time required for data preparation, acquisition, and analysis.

DanioScope performs video-based analysis, automatically detecting zebrafish embryos within their chorion and minimizing the need for manual intervention. It supports batch data acquisition from a list of videos and can handle situations where animals move slightly by combining measurements taken at different locations on the animal.

Embryo Activity Measurements

• Detects and quantifies movements such as tail flicks, coilings, and convulsive behavior, which begin as early as 17 hours after fertilization
• Automatically recognizes each embryo within its chorion from video input
• Allows adjustment of measurement location if floating occurs during the experiment
• Reports burst activity as a percentage of total measurement duration during which the embryo was moving
• Reports inactivity as the percentage of time without movement
• Reports burst duration as the total time spent active across all movement events
• Reports inactivity duration as the total time spent inactive
• Reports burst count as the number of discrete movement events
• Reports burst count per minute as the rate of movements over time

Cardiovascular Measurements

• Assesses heart rate and inter-beat intervals using video-based analysis, replacing labor-intensive manual methods such as stopwatch counting, micro pressure systems, Laser Doppler microscopy, and electrocardiograms
• Automatically calculates beats per second (BPS) and beats per minute (BPM) after the user indicates the heart area in the imported video
• Supports cardiology research by leveraging the developmental similarity between the zebrafish and human cardiac systems

Blood and Gut Flow Measurements

• Measures blood flow in a selected vessel using frame-by-frame pixel change analysis, avoiding the need for fluorescence labeling techniques
• Measures gut flow using the same video analysis approach
• Requires the user to select the region of interest from wall to wall within the video image
• Presents blood or gut flow as an activity percentage

Morphology Measurements

• Supports upload of images or extraction of snapshots from videos for morphological analysis
• Provides intuitive drawing tools for defining distances and areas of interest
• Automatically measures lengths and surfaces after calibration, including tail length, eye size, and pericardial area
• Allows users to define custom measurements beyond the built-in options
• Enables monitoring of growth and malformations over time using images from different time points

Software Features and Data Handling

• Supports high-speed video input at over 60 frames per second
• Compatible with a wide range of video formats
• Offers options for data selection, visualization, and analysis after acquisition
• Allows raw data export for further analysis in external statistical software
• Supports combining multiple measures on a single animal
• Includes batch acquisition for processing multiple videos
• Provides flexible tools for selecting, grouping, and displaying data
• Allows redefinition of thresholds to fine-tune results
• Includes experiment handling and organization tools to simplify setup and execution

DanioScope has been used across a range of research applications and has been cited in numerous publications. It functions as an all-in-one tool covering activity, cardiovascular, flow, and morphology measurements within a single platform.