Convert image to objects

Converts objects encoded in a labelled image stack back into objects.

Description

Converts objects encoded in a labelled image stack back into objects. Each output object is comprised of all pixels in a single timepoint with the same pixel intensity. As such, pixels need not be in direct contact to be assigned the same object. For objects tracked through time, the image intensity can be interpreted as the ID of a parent track object.

Note: This module has different behaviour to the "Identify objects" module, which takes a binary image, identifies contiguous foreground regions and assigns new object IDs.

Parameters

Parameter	Description
Input image	Labelled image to convert to objects. The background (non-object region) of this image should be black (0 intensity) and all pixels corresponding to the same object should have the same value. Objects can only exist in a single timepoint, so pixels of the same intensity but in different timepoints will be assigned to different objects.
Output objects	Output objects created by the conversion process. These will be stored in the workspace and be accessible via this name.
Volume type	The method used to store pixel coordinates. This only affects performance and memory usage, there is no difference in results obtained using difference storage methods. "Pointlist" (default) stores object coordinates as a list of XYZ coordinates. This is most efficient for small objects, very thin objects or objects with lots of holes. "Octree" stores objects in an octree format. Here, the coordinate space is broken down into cubes of different sizes, each of which is marked as foreground (i.e. an object) or background. Octrees are most efficient when there are lots of large cubic regions of the same label, as the space can be represented by larger (and thus fewer) cubes. This is best used when there are large, completely solid objects. If z-axis sampling is much larger than xy-axis sampling, it's typically best to opt for the quadtree method. "Quadtree" stores objects in a quadtree format. Here, each Z-plane of the object is broken down into squares of different sizes, each of which is marked as foreground (i.e. an object) or background. Quadtrees are most efficient when there are lots of large square regions of the same label, as the space can be represented by larger (and thus fewer) squares. This is best used when there are large, completely solid objects.
Create track objects	When selected, the intensity of the image for each object will be assumed as corresponding to the ID of a parent track object. This allows track relationships for objects present in multiple timepoints to be loaded back into MIA.
Output track objects name	If creating track objects ("Create track objects" is selected), this is the name of the output tracks. These will be parents of the output objects.