Knowledge Base

Questions and Answers

General

• How DanioScope analyzes video images
• Change the default data folders
• Which video and image formats are supported?
• Create a copy of data
• Copy settings from one experiment to another

Embryo Detection

• How to deal with embryo movements in space

Measurements and Shapes

• Add a measurement
• Delete a shape (measurement or subject)
• Add a new subject
• Duplicate a shape
• Change the shapes' color
• Zoom in/out
• Edit the independent variable values

Analysis Results

• Remove results for a video or subject

See Also

• Error messages
• For more information

How DanioScope Analyzes Video Images

Pixel Change in the Area of Interest

For Activity, Cardiology and Flow measurements, DanioScope analyzes the change in gray scale values of each pixel in the areas of interest (for example, in the case of Cardiology, the heart area).

A pixel is the fundamental unit of a digital video or still image. Its gray scale value varies from 0 (pure black) to 255 (pure white). For each video frame n, a value of Activity (%) is calculated. This is the percentage of pixels in the area of interest that change their gray scale value relative to the previous frame (n-1), is the value of Activity (%) for frame n.

Example

In the example below, two pixels are considered within the embryo area (for Activity). One pixel (top) changes between two video frames. The other (bottom) does not.

Suppose that the embryo area defined by the yellow circle is 1000 pixels. If the number of pixels that change their gray scale value from video frame n-1 to video frame n is 450, then Activity (%) for frame n is 45%.

For Activity, Cardiology and Flow, the output parameters are based on the temporal change of Activity (%). See a few examples in Visualize Data.

Missing Video Frames

What Are Missing Video Frames?

When recording digital video, the recording hardware and software may not take all information it is given. This may happen when recording high resolution video at high frame rates. In such cases one or more video frames may be "dropped", or "missing". Whether a video file contains missing video frames also depends on the recording setup.

If video contains consecutive missing frames for less than 0.1 s, DanioScope linearly interpolates the values of Activity (%) from the known values of the neighboring frames. The measurement is marked as Acquired.

Example of How DanioScope Deals with Missing Frames

A measurement is defined in part of a video which contains two consecutive missing frames. Two missing frames for a video of 25 frames per second are equal to 2 x 0.04 = 0.08 s.

The adjacent (valid) video frames are analyzed and their Activity (%) values are 10 and 30, respectively. The interpolated values of activity for the two missing frames are 17 and 23, respectively.

Note, however, that if the same measurement included 4 or more consecutive missing frames, it would not be analyzed and Video error would appear under Status in the Measurement list.

Notes

• If you analyze video from time 0.00 (first video frame), the value of Activity (%) at that time is unknown. This is because at that time there is no previous frame as a reference.
• If you analyze video from a non-zero time, the value of activity at that time is known, because there is always a previous frame.
• If you analyze video from time t1 to t2, activity is calculated for all frames, including t1 (unless t1 = 0) and t2.

Change the Default Data Folders

To change the default location for data, export and backup files, choose File > Preferences. Select a new folder:

• To change the location of future experiments, click Browse next to Experiments.
• To change the export folder, click Browse next to Export.
• To change the default backup folder, click Browse next to Backups.

Which Video and Image Formats Are Supported?

Video Formats (for All Functions)

• MPEG-1
• MPEG-2 — This is a collection of formats; not all are supported.
• MPEG-4 — This is a collection of formats; not all are supported.
• H.264 AVC — This is a type of MPEG-4, which is supported.
• DV-AVI — This is uncompressed video from FireWire cameras. This format is not recommended because of the large file size. Note that DV-AVI is a special case of AVI. In general, DanioScope does not support AVI files. Also, the AVI format should not be confused with the *.avi file extension. Some MPEG-4 files have the extension *.avi, which DanioScope does support.
• QuickTime — Container file format developed by Apple. QuickTime video is usually stored in files with MOV extension, and commonly uses the MPEG-4 codec for compression.
• Windows Media Video — With file extension *.wmv.

Notes

• File extensions supported are: avi, mpg, mpeg, mp4, mov, wmv.
• Video files made with Media Recorder are supported.
• Flash video files (*.flv) are not supported.
• Important: Test a specific format before recording all the videos for your experiment. To test a video format, in the Acquisition screen load the video file and play it back. Define one or more measurements, acquire data and check that error messages are not given. See Error Messages.
• Automatic detection of embryos for Activity analysis is only possible when the video is not distorted relative to the original aspect ratio of the camera image. If that is the case, convert the video to a compatible format and adjust the video aspect ratio.

Image Formats (for Morphology)

• JPEG — With file extension *.jpg.
• Bitmap — With file extension *.bmp.
• Portable Network Graphics — With file extension *.png.