Operation XML with Flat Bounding Box

This page evaluates the "Operation XML element ROIs" use case expressed on the Roi5D Proposals OME-XML-Model-2005-ROI5D page with respect to the Flat Bounding Box OME-XML-Model-2005-Flat-Bounding-Box data model.

Representation

Arbitrary, user-specified (during acquisition) area in 2D (generally some sort of blob), at a given Z plane

This structure can be expressed as a 5DBoundingBox object with XY extents corresponding to the blob's bounding box, and startZ=endZ at the correct Z plane. Since the Operation presumably occurs at a particular time, there would also be startT=endT for the time point when it occurred. As for C, startC=0 and endC=numC-1 (i.e., all channels) is probably sufficient. The 5DBoundingBox's linked Shape could be a Rectangle in the simplest case, or a Polygon, or a BinaryMask, depending on the blob's complexity.

(I am not completely clear on what constitutes a 2DBoundingBox or 3DBoundingBox object, so I will not comment on whether those structures would be more appropriate.)

Operation to which this area corresponds (e.g., a particular attempt at photobleaching)

This characteristic is represented by a reference within the Operation XML element to the desired 5DBoundingBox expressed in XML.

Potentially in the future, user-specified enumeration of these areas across multiple Z planes

This scenario can be handled by expanding the startZ/endZ range to include more than one Z plane. If we eventually define 3D shapes (such as a 3D bitmask), we can link that 3D shape to the 5DBoundingBox.

It is my understanding that we will not need to express a discontinuous collection of Z planes. But if we did for some reason, it would be easily handled by having the Operation reference a RegionUnion instead of a single 5DBoundingBox. This solution would also allow the specification of a series of 2D bitmasks (or rectangles or polys) to define the shape instead of a single 3D shape.

Specific queries encapsulating the questions

For a given operation, what is the corresponding targeted area?

This query is easy — the Operation has a Shape attribute that references a specific 5DBoundingBox (or RegionUnion), which identifies the targeted area.

For a given Z plane, what operations took place?

From the list of 5DBoundingBoxes linked from Operations, select all 5DBoundingBoxes such that the Z plane lies within the Z extents.

For RegionUnions, one more layer exists. The RegionUnions linked from Operations must have each constituent 5DBoundingBox checked to see if the Z plane lies within the Z extents of that bounding box. If so, the RegionUnion qualifies.

For a given area on a specified Z plane, are there any operation ROIs that overlap? (probably less important)

This query is harder. An appoximation is not too difficult: from the operations that took place on that Z plane (see above query), select all 5DBoundingBoxes such that the given area rectangle overlaps with the bounding box in X and Y (I can post the math for this if necessary).

If the given area is non-rectangular, or the 5DBoundingBox's linked shape is nonrectangular, or both, the query becomes more difficult. Different types of shapes require different cases. In the bitmask case, checking for overlap simply entails finding a single pixel in X and Y that is included for both the given area and the operation's bounding box. But this test is not cheap if there are many operations to analyze.