# ROI discussion proposal

Roger's doc sent to nitpick

ROI.txt — Plain Text, 5Kb

## File contents

ROI Discussion ############## ROIs in three dimensions ------------------------ This is just a followup regarding discussion with J-M and Will earlier today, where we covered the possibility of adding support of 3D primitives to the model. (Note that opinions over what to add remain divided, and this certainly needs further discussion!) These are just my thoughts on how we might add initial support. [Note that for the n-dimensional stuff, I just added it as something to think about--I'm not suggesting we add any support at this point.] +---------------+-----------------------+---------------------------+ |2D | 3D | nD | +===============+=======================+===========================+ |Line [2DLine] | 3DLine | nDLine | +---------------+-----------------------+---------------------------+ |Rectangle | 3DCube [Cube] | nDCube [Hypercube] | +---------------+-----------------------+---------------------------+ |Ellipse | 3DEllipse [Ellipsoid] | nDEllipse [Hyperellipsoid]| +---------------+-----------------------+---------------------------+ |Point [2DPoint]| 3DPoint | nDPoint | +---------------+-----------------------+---------------------------+ |Mask | 3DMask | | +---------------+-----------------------+---------------------------+ |Path [2DPath] | 3DPath | | +---------------+-----------------------+---------------------------+ |Mesh [2DMesh] | 3DMesh | | +---------------+-----------------------+---------------------------+ |Text | | | +---------------+-----------------------+---------------------------+ Currently, the ROI model only supports 2D shapes. In the above table, additional primitives for 3D (and nD) have been added. Due to the "3D" or "nD" prefix, these do not replace the existing 2D-only primitives for backward compatibility, and to make it clear that these are for 3D work. Note that the "nD" primitives would work in 2D, 3D and higher dimensions; the existing primitives could all be implemented in terms of nD primitives in the code, but it is useful to have fixed-dimension primitives in the model. Some of the 3D primitives described below may appear to be redundant; it's certainly possible for example, to represent a shape in 3D right now using multiple shapes, one per z plane. However, being able to use native 3D primitives is more powerful: it permits additional measurements involving volume, surface area and shape. At a higher level, the same is implied for e.g. cell tracking in xyzt; being able to draw a single polyline line (or vector), rather than storing a single point or line at each timepoint results in us being able to compute velocity and direction changes directly--rather than having to compute this information from discrete shapes, the information is directly available in a single shape. I've also noted that some shapes may be represented equivalently in different ways; it might be worth considering adding support for these because it firstly allows the shape to be computed in different ways, which can differ depending upon the problem being solved, and it also contains information about how the measurement was made, i.e. the intent of the person doing the measuring, which is lost if converted to a canonical form. Basic 3D primitives ------------------- **3DLine** List of (x,y,z) vertices. Alternative representation: a single vertex and list of vectors. **nDLine** List of e.g. (x,y,z,t) vertices (tracking movement including speed and direction changes). Alternative representation: a single vertex and list of vectors. **3DCube** X,Y,Z,Width,Height,Depth The current representation is effectively a vertex and a vector. Alternative representation: Both Rectangle and 3DCube could be represented by two vertices. **nDCube** Vertex + Vector Alternative representation: two vertices. **3DEllipse** X,Y,Z,RadiusX,RadiusY,RadiusZ This representation is effectively a vertex and a vector. Alternative representations: - two vertices, - vertex + vector - single vertex and the Mahalanobis distance [most useful when computing distributions with covariance; enables rotation with n-1 degrees of freedom] **nDEllipse** Same as for 3DEllipse alternative representations **3DPoint** X,Y,Z **nDPoint** X,Y,Z,... Bitmasks -------- **Mask** Could we have a pointer to an IFD/file reference plus two coordinates so specify a clip region, then we can pack potentially hundreds of masks in a single plane. **3DMask** As for Mask, but in 3D. A 3DMesh could be computed from a 3DMask. Meshes ------ **Mesh** 2D mesh described as e.g a face-vertex mesh. **3DMesh** 3D mesh described as e.g. a face-vertex mesh. Meshes could be computed from masks, polygons, extruded shapes where there is a z range, or from thresholding. Paths ------ **3DPath** As for Path, but with additional vector to describe motion along the prescribed plane? Transforms ---------- To support proper 3D operation, it would make sense to extend the existing support for 3×3 2D affine transforms to 4×4 3D transforms.