Modules

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
Save location Select where the image should be saved.
  • "Mirrored directory" Save the image to a new directory structure which has the same layout as the input. This is useful when batch processing from a multi-layer folder structure. The subdirectory layout will match that of the input structure, but will have its root at the folder specified in "Mirrored directory root".
  • "Match Output Control" Save the image to the folder specified by the "Save location" parameter in "Output control".
  • "Save with input file" Save the image in the same file as the root file for this workspace (i.e. the image specified in "Input control".
  • "Specific location" Save the image to a specific folder.
Mirrored directory root The root path for the mirrored directory structure. This path is the equivalent of the folder specified in "Input control". All subfolders will be in the same relative locations to their input counterparts.
File path Path to folder where images will be saved.
File name (generic)
Save name mode Controls how saved image names will be generated.
  • "Match input file name" Use the same name as the root file for this workspace (i.e. the input file in "Input control".
  • "Specific name" Use a specific name for the output file. Care should be taken with this when working in batch mode as it's easy to continuously write over output images.
File name Filename for saved image. Care should be taken with this when working in batch mode as it's easy to continuously write over output images.
Append series mode Controls if any series information should be appended to the end of the filename. This is useful when working with multi-series files, as it should help prevent writing files from multiple runs with the same filename. Series numbers are prepended by "S". Choices are: None, Series name, Series number.
Append date/time mode Controls under what conditions the time and date will be appended on to the end of the image filename. This can be used to prevent accidental over-writing of images from previous runs:
  • "Always" Always append the time and date on to the end of the filename.
  • "If file exists" Only append the time and date if the results file already exists.
  • "Never" Never append time and date (unless the file is open and unwritable).
Add filename suffix A custom suffix to be added to each filename.
Input image Image onto which selections will be drawn. This will be displayed automatically when the module runs.
Add existing objects
Input objects
Allow missing objects
Apply existing class
Metadata item for class
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).
Assign classes
Classes source
Class file
Allow additions
Class list (comma-separated)
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, Single point, Wand (tracing) tool.
Point mode (point-type ROIs only)
Message on image Message to display in title of image.