Knowledge Base

Create a Copy of Data

Aim

With the Backup function you can create backup copies of experiments to store data in a safe location.

Important: A backup of the experiment does not contain video and images. Do not forget to create backup copies of these as well.

To Back Up an Experiment

1. Open the experiment you want to create a copy of, and choose File > Make Backup. Enter a File name. Choose a Folder. The default folder is C:\Users\Public\Documents\Noldus\DanioScope\Experiments\Backups. Click Backup.
2. Copy the backup file (with extension *.dsz) to the location you require. If you want to open the experiment on another PC, make sure to copy the video and images together with the *.dsz file.
3. To restore an experiment from a backup file and open it in the new location, choose File > Restore Backup. Choose the backup file and select the folder where you want to store the experiment. If DanioScope does not find the videos/images, click Relink Videos/Images and select the folder where you copied your videos/images.

Notes

• Important: Make a backup of your experiments on a regular basis, at least once a day.
• The default name of the backup file is [experiment name] - [date] [time].dsz.
• To change the default backup folder, choose File > Preferences.
• Click Open Output Folder in the Backup Experiment window to check which backup files are saved there.

Copy Settings from One Experiment to Another

Aim

With the Template function you can save settings like morphology measurements and independent variables to a template, and apply those settings when creating new experiments.

To Save an Experiment as a Template

A template is an experiment with predefined settings, but no video or data. You can use a template to create new experiments with the same settings and properties without having to re-define them.

When you save an experiment as a template, the template stores the following:

• The Measurements selected in the Experiment Settings.
• The list of Morphology Measurements.
• The list of Independent Variables.
• The Activity Settings.
• Calibration Profiles.

To save an experiment as a template, open that experiment and choose File > Save as Template. Enter a name and click OK.

To make an experiment based on a template, choose File > New from Template.

Manage Your Templates

• To rename or delete a template, choose File > Manage Templates, select the template and click Rename or Delete.
• To specify a template as a default, choose File > Manage Templates, select the template and click Set as Default. That template is selected when you create an experiment from a template.

The Standard Template

The standard template has the following settings:

• Measurements: Choose Setup > Experiment Settings to view the default measurements.
• Independent Variables: Choose Setup > Independent Variables.

How to Deal with Embryo Movements in Space

Depending on your medium, embryos might float to another location during the experiment. When this happens, you can redefine the position of the embryo and measure activity at this area for the selected duration of the video.

Example

In this example, the subject S01 stays in the same place between time A and B (the arrow represents time), then from time B to C it moves to the right of the image. From time C, it stays in the same position up to the end of the video. For accurate activity quantification, the yellow circle must overlap with the chorion. Therefore, the measurement S01/M1 must be defined from frame A to B. You can do this by setting the stop time to time B. See To Set a Stop Time for a Measurement below.

Since the embryo does not displace from time C to the end of the video, you could add a second measurement that goes from time C to the end of the video. Note, however, that if you work with large samples, occasional floats may be ignored. You can minimize the amount of manual editing and keep your margin of error low.

To Set a Stop Time for a Measurement

1. Position the video to the last frame where the subject remains in the initial position.
2. Click that subject's name in the subject list, and click the button under Stop. The Stop time changes to the current video time for that subject. The Duration of the video fragment to analyze changes accordingly.
3. To check that DanioScope does not analyze the frames after the Stop time for that subject, play the video a few frames forward. The shape for that subject should disappear.
4. If you want to analyze the video fragment after the subject has moved to its new position, see below.

Note: Video is analyzed from Start to Stop (included).

To Add a New Measurement for the Same Subject

1. Position the video to the frame where the subject has reached its new position (time C in the picture above).
2. Draw a shape around the subject/organ.
3. In the context menu, select the subject you require.
4. A new row is appended to the list, under the subject, and marked in the Measurement column with M2 (or M3, and so on, depending on how many measurements are defined for that subject). The new measurement has a Start time, a Stop time and a Duration.

Note: Video is analyzed from Start to Stop (included).