Working with objects
The previous sections described the nature of objects, why they exist, and how to use them.
This section ends with some practical tips for working with objects.
It's possible to independently change whether TMA cores, annotations or detections are displayed, and also to independently switch whether annotations or detections are shown as outlines or filled. In terms of display, tiles more or less follow detections (since they are special examples of detections) and use the same commands to control them, since you generally only have one or the other. The same is true of cells, except that there are options available to change whether cells are viewed with/without nuclei, or as nuclei only.
The display of objects can be changed in multiple ways. Some (e.g. to adjust cell display) are accessible by right-clicking on the image or within the View menu. However, the most common adjustments are accessible using shortcut keys:
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Show and hide annotations - shortcut A
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Show and hide a TMA grid - shortcut G
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Show and hide detections - shortcut H (for 'hide') -
Fill and unfill detections - shortcut F
Once created, detections can't be edited. Annotations and TMA cores can usually be edited, for example by moving or resizing them. However, this isn't always the case, because sometimes editing an existing annotation or TMA core accidentally could confuse things. The main example is if detections are made within a TMA core or annotation, then we normally want the parent to remain fixed in place from that point on - and not shifted arbitrarily to no longer coincide with the detection it contains. For this reason, TMA cores and annotations can sometimes be locked. Locking almost always takes care of itself without you needing to worry about it, but if you want more control then right-clicking on an annotation gives an option to lock or unlock it.
The annotation on the left is selected and unlocked. You can tell because the little squares are 'handles' useful for resizing.
The annotation on the right is selected and locked. Note: no little resizing handles. It was locked because it was used as the ROI when creating the detections inside.
Right-clicking on a locked annotation gives the option to unlock it...
...although you probably don't want to do this, since then moving the newly-unlocked annotation can be confusing.