Regions of Interest and Manual Annotations

QuPath has two main types of objects, Annotations which are generally for large areas like 'tissue' or 'tumor' and Detections which are for small objects like cells or spots. The main difference between these two object types is really in how they are used, annotations for large flexible regions that are both manually editable and can serve as containers for other objects, and detections for when you need thousands or even millions of locked in objects that will not crash your computer.

1. Here we will look at the annotation tools and how to use them.

1. The video goes through each type of annotation and a little bit of information about how to use them.

2. Certain keys can modify the actions of annotations:

1. ALT to become an eraser

2. CTRL+SHIFT to draw up to but not across existing annotations

3. SHIFT to lock certain object types to fixed relative dimensions, like keeping the ellipse tool a circle or the rectangle tool a square

4. CTRL+Z to undo an action - only a limited number of actions are tracked, and this number decreases rapidly with the number of vertices in the annotations moved. Do not expect much leeway for very complex annotations like high resolution tissue borders.

2. Selecting objects - double click to select most objects. If they are stacking within one another, it takes an extra click to get each subsequent object. For example, if you have an annotation with a cell in it, double clicking on the cell will select the annotation, while triple clicking the cell will select the cell. The Selection tool is mentioned at the end of the video, and essentially it can be toggled on to allow you to manually draw a temporary outline that selects all objects inside of it when the left mouse button is released.

3. The annotation tools are best demonstrated in the video.

4. Classes can be added to any annotation through the right click context menu, or a variety of other ways including the 'Set class' button in the Annotations tab, SHIFT+Right click on the object and select the class color, scripting, and more.

5. Toggling on the Auto set button within the Annotations tab means that each newly created annotation will use the currently selected class in the annotation menu. If that is “None”, you will see the default behavior. However, if you have “Tumor” selected, all subsequently created objects will be automatically classified as “Tumor”. This, combined with turning off the Return to Move tool automatically in the Preferences can make manually annotating many objects for deep learning projects much, much faster.

   1. When Return to Move Tool is toggled off, remember to hold down the space bar when you want to left click and drag to move without drawing!