Create a polygonal region of interest with the pen tool:

1. Select the "Pen" tool in the list of annotations and ROIs (See "How to create 2D annotations").





2. Bring your mouse above one image in a display area and press the left button to start the freehand draw of the polygon.
3. While holding the left mouse button, move your mouse to add new points to the polygon.
4. Release the left button of the mouse to close the polygon.

Some information about this region of interest will be displayed in the bottom right corner of the image. The default displayed information depends on your settings in the preferences panel.

Modify the freehand polygon position:

1. Select the freehand polygon ("pen" object) by clicking on it with the left mouse button. When a freehand polygon object is selected, its outline is a yellow dotted line.
2. Keep your mouse above the polygon, press the left mouse button and hold it.
3. While holding the left mouse button, drag your mouse to move the location of the freehand polygon.
4. Release the left button of the mouse.

All information about the freehand polygon will be recalculated and displayed in the bottom right corner of the image.

Modify the properties of the freehand polygon ("pen" object):

1. Select the freehand polygon ("pen" object) by clicking on it with the left mouse button. When a freehand polygon object is selected, its outline is a yellow dotted line.
2. In the properties window of annotations and ROIs, modify the color or the width of the freehand polygon. You can also modify the displayed information and use some threshold values for the calculation of its surface and other data such as the average pixel values.

Mark one or more of the checkboxes in front of the area, center, min/max, total, mean or standard deviation to display the corresponding values in the bottom right corner of the image.

Use of the minimum and maximum threshold:

1. Mark the "Display" check box. This will add a colored layer inside the freehand polygon ("pen" object). This layer marks the pixels in the polygon, which belong to the range defined by the minimum and the maximum threshold.
2. Mark the "Min Threshold" check box.
3. In the "Min Threshold" edit box, type the minimum threshold value and hit the 'Enter' key.

Note that the surface area, min/max, total, mean and standard deviation values have been affected by the new minimum threshold. Some pixels in the freehand polygon are also no more in the green layer.

You can modify the minimum threshold in a more interactive way by following these instructions:

1. Keep your mouse cursor in the "Min Threshold" edit box, press the right button of the mouse and hold it.
2. While holding the right button, drag your mouse in the left direction to decrease the threshold value or in the right direction to increase it. As you drag, you can see the green layer and values affected in real-time.
3. Release the right button of the mouse.

Note:

• To use the maximum threshold value, please follow the same instructions than for the minimum threshold.
• When you use the minimum or maximum threshold value, the calculation of the surface area will be based on the pixel surface area unit. When not, the calculation of the surface area is based on the real size of the freehand polygon. Both values may differ a little.
• You can modify the color of the layer in the preferences panel.