Manually identify objects

Manually create objects using the ImageJ selection tools.

Description

Manually create objects using the ImageJ selection tools. Selected regions can be interpolated in Z and T to speed up the object creation process.

This module will display a control panel and an image onto which selections are made.

Following selection of a region to be included in the object, the user can either add this region to a new object ("Add new" button), or add it to an existing object ("Add to existing" button). The target object for adding to an existing object is specified using the "Existing object number" control (a list of existing object IDs is shown directly below this control).

References to each selection are displayed below the controls. Previously-added regions can be re-selected by clicking the relevant reference. This allows selections to be deleted or used as a basis for further selections.

Once all selections have been made, objects are added to the workspace with the "Finish" button.

Objects need to be added slice-by-slice and can be linked in 3D using the "Add to existing" control.

Parameters

Parameter	Description
Input image	Image onto which selections will be drawn. This will be displayed automatically when the module runs.
Output objects	Objects created by this module.
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.
Spatial interpolation	Interpolate objects in Z. Objects assigned the same ID will be interpolated to appear in all slices between the top-most and bottom-most specific slices. Specified regions must contain a degree of overlap (higher overlap will give better results).
Output tracks	When selected, the same object can be identified across multiple timepoints. The same ID should be used for all objects in this "track" - this will become the ID of the track object itself, while each timepoint instance will be assigned its own unique ID. This feature also enables the use of temporal intepolation of objects.
Output track objects	Name of track objects to be added to the workspace. These will be parents of the individual timepoint instances and provide a way of grouping all the individual timepoint instances of a particular object. Track objects themselves do not contain any coordinate information.
Temporal interpolation	Interpolate objects across multiple frames. Objects assigned the same ID will be interpolated to appear in all frames between the first and last specified timepoints. Specified regions must contain a degree of overlap (higher overlap will give better results).
Instruction text	Text that will be displayed to the user on the object selection control panel. This can inform them of the steps they need to take to select the objects.
Default selector type	Default region drawing tool to enable. This tool can be changed by the user when selecting regions. Choices are: Freehand line, Freehand region, Line, Oval, Points, Polygon, Rectangle, Segmented line, Wand (tracing) tool.
Point mode (point-type ROIs only)
Message on image	Message to display in title of image.