Knowledge Base

Workflow

Record Media Files

Record video and/or images of one or more subjects to digital media files of compatible format.

Video image quality is very important for automatic detection of embryos (see Video Image Quality). If automatic detection does not work, draw manually the contour of the embryo.

Give your media files unique names, in such a way they suggest which subjects and time points are recorded. This is handy when copying files from one computer to another.

Setup

Experiment Settings. Choose which type of measurement you want to carry out: Activity, Cardiology, Flow and Morphology. For Morphology, define the measurements you want to take; for example the Body length.

Independent Variables. Define for example the experimental groups Control, Concentrate 1, and Concentrate 2, or variables that mark subjects, for example Batch number. You can use independent variables to make analysis groups.

Acquisition

Load the videos you want to use (or pictures, in the case of Morphology), define the areas of interest or, in the case of Activity, let the program detect them for you.

For Activity, Cardiology and Flow, click Acquire. For Morphology, calibrate the pictures according to your camera setup and take the measurements.

Analysis

Data Selection (optional). Select measurements based on the values of your Independent Variables. By default, all subjects and measurements are selected for analysis.

Visualizations. Visualize data for inspection. For example, plot the power spectrum for cardiology measurements. Replay the video and data together.

Trial Statistics. Let DanioScope calculate the statistics of your measurements. For example, the average activity level or average heart rate of each subject.

Group Statistics and Charts. Let DanioScope calculate statistics averaged over the subjects in a group. For example, the average heart rates for the three groups Control, Concentrate 1 and Concentrate 2. Summary statistics are accompanied with charts.

Result Export

Export the results table to text or Excel format. You can export both Trial statistics and Group statistics.

For Activity, Cardiology and Flow you can also export the raw data to other software to analyze short-time changes in detail.

Video Image Quality

Please read the following recommendations carefully.

Video and Image Files

• Make sure that the video or still image has good contrast and focus.
• Check that the image aspect ratio is not distorted relative to that of the source camera. When you load the video files in DanioScope, the chorion should be circular, not egg-like. If the image is distorted, convert the video to adjust the aspect ratio. The aspect ratio of an image describes the proportional relationship between its width and its height. It is commonly expressed as two numbers separated by a colon, for example 4:3 like in still camera images or standard television, or 16:9 like in high-definition television.
• DanioScope may not analyze video when it contains missing frames. To reduce the probability that your video contains missed frames, keep a video frame rate just enough to give you the information you need, not higher. One of the causes of missing frames is the shutter (exposure) time in the camera that is too high to be compatible with the frame rate. In that case the camera must keep the shutter open for a long time, and does not have the time necessary to read each video frame at the expected rate. See the documentation that comes with the camera for how to adjust the exposure settings.

Test Environment

• Embryos should be on a uniform background. Always place embryos in a Petri dish.
• Make sure the substance that holds the embryo (for example, agar) does not contain air bubbles or other irregularities.

Subjects

• In order for DanioScope to detect the position of the embryo automatically, subjects must be transparent enough. This is typically the case of zebrafish embryos.
• If the chorion is hairy, automatic detection may not work all times.

What's New in DanioScope 1.1?

Supported Video Formats

You can now analyze video in QuickTime format, with MOV file extension, and Windows Media Video, with WMV file extension.

Data Management

Independent Variables

You can now enter the values of independent variables more easily:

• Directly in the video image. Right-click the subject shape and select Edit Variable Values. Hold Ctrl or Shift down to select multiple shapes.
• In the Measurement list, hold Shift or Ctrl down and click the rows for which you want to edit the values. Next, choose the value you want to assign to those measurements.

Export Raw Data

You can now export raw data, where data are written for each video frame analyzed. You can export raw data to text or Excel.

Your First DanioScope Experiment

Background

In DanioScope, an experiment is a collection of video files, data and results related to specific research questions. Each experiment is saved separately on your computer.

To Create an Experiment

1. To create an experiment from scratch, choose File > New. To create an experiment from a preexisting template, choose File > New from Template.
2. Next to Name, enter the name you want to give to the experiment. The experiment is saved in C:\Users\Public\Documents\Noldus\DanioScope\Experiments. To select another location, click Browse.
3. If you have chosen New from Template in step 1, select a template from the Template list. Default is Standard Template.
4. Click Create.

Notes

• You cannot exchange data between different DanioScope experiments. Make sure that each experiment contains all the video files and results that you want to use for a specific research project.
• To open an existing experiment, choose File > Open.
• Each experiment is saved to a file with extension *.dse, located in a folder with the same name as the experiment. The folder contains two default sub-folders, Settings and Data.