In Objects, it was stated that all objects have their own measurement lists. While true, this is not the whole story.
Different kinds of measurement
There are actually three main sources of measurements for individual objects within QuPath:
Measurement lists (static)
Shape statistics (dynamic)
Summary statistics (dynamic)
The main difference between them is whether they are static (i.e. unchanging) or dynamic (i.e. updating automatically).
Measurement lists are, as the name suggests, basically just lists of measurement names and their numeric values. These values are usually fixed when the objects is created, or added or updated by running a specific command (e.g. feature smoothing, or to add intensity features).
They are mainly important with detections, and provide the features used when training a classifier (see Cell classification).
Shape statistics are calculated for each ROI. They are mainly used with annotations and important when manually measuring structures.
QuPath can show the shape statistics for each annotation, adapted for the ROI type (e.g. length for lines, areas for areas, counts for numbers of points). They are not stored statically in measurement lists because it is possible that the ROI for an annotation changes (e.g. if it is being drawn or moved).
Summary statistics are calculated for each annotation or TMA core object based upon whatever is known about it.
This could be the number of child or descendant objects of a particular class, or the percentage of positive cells falling within it. These are important as the final output for biomaker scores, e.g. to provide Allred or H-scores.
When viewing a results table, the actual measurements can be pulled from any or all of these sources. The user generally doesn’t have to care where the measurements came from, but the distinction is crucial when scripting or trying to decipher the details of what is going on.
Of particular importance, measurement lists need to be explicitly updated and so should be used for ‘permanent’ measurements. The other measurements need to be calculated dynamically.
In this regard, it is strongly preferable that summary statistics are dynamic because it’s usually the case that the numbers and classifications of descendant objects could change at any moment… and it’s essential to ensure that when a parent object is asked for summary measurements, they are always up-to-date.
The summary statistics are based upon the detection objects descended from the annotation. More information is given in Object hierarchy.
A warning about summary statistics
It is important to be aware that not all summary measurements are necessarily dynamic. The most common ones for pathology that are built-in to QuPath (e.g. H-score, Positive %) are dynamic, but others that are added elsewhere may not be. It really depends upon how the person who wrote the code to make the measurement designed it.
For example, if you run a particular script to calculate a new measurement somewhere, it is possible that it creates a static measurement and adds it to a measurement list - in fact, this is actually quite likely, because it is easiest for the developer of the script to do it this way. This means that, if you want this measurement to be updated later whenever you make further changes, you probably need to run the script again.
Therefore be careful with measurements, and try to always check that you have definitely measured what you think you have, e.g. by moving or deleting an object that you predict should have an effect on the measurement to see if the measurement in question updates (i.e. it is dynamic) or not.
Because this can be confusing, in the future QuPath may make it clearer when measurements are dynamic and when they are not. It is also planned to make it easier for developers to write their own dynamic measurements.