Knowledge Base

Setup

Experiment Settings

To access the Experiment Settings, choose Setup > Experiment Settings.

In the Experiment Settings screen you find:

• Location – The location where your experiment is saved.
• Description (optional) – Enter information about your experiment such as the kind of test that you perform, the date video was recorded, the name of the researchers, etc. You can edit the description at any time.
• Measurements – DanioScope offers four types of measurements. Choose one or more of the following:
  • Activity. To measure activity bursts.
  • Cardiology. To measure heart rate.
  • Flow. To measure fluid movement rate in a blood vessel or the gut.
  • Morphology. To measure body parts and organs. If necessary, edit the list of Morphology Measurements.

What you select under Measurements determines what items are listed under Acquisition in the Experiment Explorer.

To enter text you can use a wide range of Unicode characters. For details, see: http://en.wikipedia.org/wiki/Plane_(Unicode)#Basic_Multilingual_Plane.

Morphology Measurements

To access the Morphology Measurements, in the Experiment Settings, under Measurements select Morphology.

The list contains predefined measurements when you create a new experiment from scratch or from the Standard Template:

• Body Length (in m). Measured as you draw the line Body Length.
• Eye Size (in m²). Measured as you draw the area of interest Eye Area.
• Pericardial Area (in m²). Measured as you draw the area of interest Pericardial Area.

The remaining variables are for direct observation (not detected automatically):

• Somites. The observed number of somites.
• Tail Detachment. With possible values Positive and Negative.
• Body Curvature. With possible values Dorsal, Ventral, and Straight.

To Add a Measurement Variable

1. Click the Add button.
2. Next to Name, enter a short name for the variable (default: Variable).
3. From the Type list, select the type of the new variable:
   • Area. To measure the area of a surface in the subject.
   • Length. To measure the length of a body part or organ.
   • Classifier. To assign a body part to a category.
   • Number. To record the number of repeated structures.

   If you select Classifier, click Add to enter a new value. To delete a value, select the corresponding row and click Delete. To edit a value, select the corresponding row and click Rename.

4. Next to Description, enter a description of what you want to measure.

To Edit an Existing Measurement

If you want to change the name, type, or description of a morphology measurement, double-click the row of that measurement or select the row and click the Edit button. Make the necessary changes and click OK.

To Delete a Measurement

Select the row of that measurement and click the Delete button.

Independent Variables

To access the Independent Variables, choose Setup > Independent Variables.

Independent variables are variables that potentially influence the outcome of your experiment. You can assign values of independent variables to each subject; for example the level of the experimental treatment or the age of the embryo. You can use the independent variables as grouping factors.

Default Independent Variables

For experiments created from scratch (File > New) or from the Standard Template (File > New from Template), two independent variables are defined:

• Compound, with 3 possible values (levels): Control, Concentrate 1, and Concentrate 2.
• Time point, with possible values 24 hours post fertilization (hpf), 48 hpf, 72 hpf, 96 hpf, 120 hpf, and 144 hpf.

Please note the following:

• Each subject can be associated with a combination of values of the independent variables. For example, Subject 1 is assigned to Control and 48 hpf; Subject 2 is assigned to Concentrate 1 and 48 hpf.
• If a subject is measured in multiple sessions in a video (called measurements M1, M2, etc.), all measurements within that video are associated with the same values of the independent variables.
• For each independent variable, specify which function that variable is used for. Select one or more of the functions available (Activity, Cardiology, Flow, and Morphology).
• Values of independent variables, including numbers, are always exported as text.

To Add an Independent Variable

1. Click the Add Variable button.
2. In the Add Variable window, enter the name of the new variable.
3. Click the Add button and enter the name of a value (level of the factor). Repeat this step for each possible value.
4. When ready, click OK.
5. A new row is appended to the list. Select for which type of measurements the new variable is used.
6. Optional: Click the cell under Description and enter any useful information about that variable.

To Edit an Existing Independent Variable

• To edit the name of a variable, double-click the name under Independent Variables and enter the name you require.
• To add or remove values of a variable, for example to replace Dose 1 with 0.01 mg or add Dose 3, click the button under Values. In the Edit Values window that appears:
  • To modify a value, select that value and click Rename.
  • To add a value, click Add and enter the value you require.
  • To delete a value, select that value and click Delete.

To Remove an Independent Variable

Select a variable name and click the Delete Variable(s) button. To select multiple variables, hold the Ctrl key down and click each variable row.

Source: DanioScope 1.1 Reference Manual - Setup, Noldus Information Technology