Knowledge Base

Morphology

Aim

In DanioScope, Morphology measures body parts and organs. Typical measurements are Body length, eye area, pericardial area. You can also define additional measurements.

To Open the Morphology Screen

Choose Acquisition > Morphology.

The Morphology module works with image files or video files.

Main Steps

1. Add images for Morphology.
2. Calibrate the images for Morphology.
3. Measure organs in Morphology.

Note: Only calibrated images are used in the statistics calculation.

Add Images for Morphology

To Add Images from Image Files

1. Click the Add Images button and load the files you require (*.bmp, *.jpg, *.png).
2. The list of loaded images appears under Morphology. The video window on the right shows the last loaded image.
3. Optional: Enter text for a Description of an image (last column of the list).

To Add Images from Video Files

1. Click the Add Images from Video button.
2. Select a video file.
3. In the Add Video Images from Video window, play the video to the point where a good image is suitable for measurements.
4. Click Grab Image. Repeat this step to add more images from the same video. Each new image is appended to the measurement list with the name [video file name]1, 2, ...
5. Click Browse to select another video file and add more images.

Tip: To select another image for preview, select the check box near its name.

To remove an image, click the corresponding row and click Remove Images.

Calibrate the Images for Morphology

To Calibrate Images

For each image, select the correct Calibration Profile from the list. Use a calibration profile to apply the same scale to multiple images. If you do not calibrate the images, length and area measurements will be in pixels and pixels², respectively.

To Create a New Calibration Profile

To create a calibration profile, use a picture containing an object of known size, like a stage micrometer.

1. Click the Calibration Profiles button.
2. Click Add and select an appropriate picture of format *.bmp, *.jpg, or *.png.
3. Enter a name for the new Calibration Profile, and click OK.
4. In the picture that opens, drag the arrow line to the extremes of the object of known size. Zoom in the image and choose another color for the arrow line if necessary.
5. Enter the Known distance of the object (in m).
6. Enter the Pixel aspect ratio or leave the default value (1.00). For information on the pixel aspect ratio of your images, see the documentation of the image acquisition software or hardware.

Tip: Most video cameras and microscopes have a pixel aspect ratio equal to 1. When the pixel aspect ratio is unknown, you can use free software like ImageJ to analyze your images. Alternatively, make a picture with an object of known size in both dimensions X and Y. Create a new calibration profile, and draw a line first over X and then over Y. Take note of the Distance in pixels (Px and Py). The aspect ratio is (Px/X) / (Py/Y).

The X Scale and Y Scale values are updated according to the values you have entered.

7. Click OK. In the Morphology screen, select the calibration profile for the images it applies to.

Note: Only images associated with a calibration profile are used in the statistics calculation.

Measure Organs in Morphology

1. Select the image in which you want to make measurements.
2. Zoom in or out when needed to have a complete view of the organ to measure.
3. Choose one of the drawing tools. The available tools depend on what Morphology measurements are defined in the Experiment Settings.
4. Draw the shape over the organ you want to measure. When drawing a polygon and the Body Length open polyline, click once to add a new vertex. To confirm the shape:
   • For the Body Length simple line and ovals, release the mouse button.
   • For the polygons, double-click the first vertex. This closes the polygon.
   • For the Body Length open polyline, double-click the last vertex.
5. Assign the shape to an existing subject or select Add Subjects.
6. For multiple subjects: If you selected Draw template shapes for all subjects, all shapes are copied at the top of the video window. Move each shape to the corresponding subject, otherwise draw new shapes and assign them to the remaining subjects.
7. Click a shape and drag its handles to resize and adapt it to the body or organ to measure.
8. For measurements that require direct observation, enter or select the value in the corresponding column of the measurement list:
   • Somites: The number of somites of that subject.
   • Tail Detachment: Select the value that applies (Positive, Negative).
   • Body Curvature: Select the value that applies (Dorsal, Ventral, Straight).
9. Repeat the procedure from step 3 to add more measurement shapes.
10. Repeat the entire procedure for each image file to analyze.

The Calibration Profile column tells you which calibration profile is used. Images marked with Not specified are not included in the analysis.

The Status column tells you which image file has been calibrated and contains measurements.

Morphology Statistics

Morphology measurements are immediately available in the list below the image window.

Note: The Status column says Partially measured when not all variables defined under Morphology Measurements are measured or entered.

See Also

• Trial statistics
• Group statistics and charts
• Export statistics

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