Image Editor


The Image Editor Tool

Figure 1: The image editor with the tools dropdown expanded and the Paint Tool displayed.

The Image Editor tool shown above is used to create and visualize segmentations interactively, as well as to correct existing segmentations (e.g. skull stripping). This tool uses the core orthogonal viewer described in Displaying Images. It has the following additional features:

Creating an Objectmap

Threshold Image Figure 2: A sample image thresholded using the Create Objectmap tool built into the editor.

You can create an objectmap in one of three ways:

  1. Load it from an existing binary file. (Under Objectmap -> Load)
  2. Create it by manually defining the regions using the Paint Tool
  3. Create it by thresholding the underlying image. Figure 2 shows the output of Create Objectmap. Note that this tool essentially performs a binary threshold.

Detailed Objectmap Operations

Image Editor Parts Figure 3: The individual components of the Image Editor.

Once an objectmap is in memory it can displayed and manipulated using tools provided in the Image Editor Tools menu.

C. The Morphology Operations tool — This performs morphological image processing operations such as erode, dilate, median, and connect (seed connectivity from current cross-hairs) etc. on 0/1 objectmaps. If the objectmap contains multiple colors then they will be converted to 0 or 1.

D. The Regularize Objectmap tool — Performs Markov Random Field Regularization to smooth manually painted regions. It was developed for the construction of the Yale Brodmann Atlas, which can be loaded under Obejctmap -> Load Yale Brodmann Atlas. To get a desired level of smoothness, set the smoothness value and press Smooth.

E. The Mask Image tool — This can be used to mask the underlying anatomical image with the objectmap to mask out all parts of the image outside the mask. Setting Inverse to On will mask the region inside the objectmap instead. Before masking, the objectmap must be binarized by thresholding it using the threshold set using the Threshold slider.

VOI Analysis Tools

VOI Analysis Figure 4: The VOI analysis window displayed over the viewer.

Given an image and an objectmap, we can generate plots of VOI image data. If the image is 4D, this tool will instead generate image timeseries plots as shown above. To invoke this control go to Objectmap -> VOI Analysis. By default, the graph shows the average intensity in each region over time. There are five buttons at the bottom which do the following:

Landmark Editor Tool

Landmark Editor Figure 5: The Landmark Editor tool.

The Landmark Editor provides functionality for manually identifying and localizing landmarks of interest within the imaging data. To invoke this control go to Tools -> Landmark Editor. By default, if no image data is loaded in the viewer, the Landmark Editor tools will be empty. The Landmark Editor tool has the following functionality:

The Current Landmark Options operate on the currently selected Point Set in Current Set:

[BioImage Suite Web Manual Table Of Contents]    [BioImage Suite Web Main Page]

This page is part of BioImage Suite Web. We gratefully acknowledge support from the NIH Brain Initiative under grant R24 MH114805 (Papademetris X. and Scheinost D. PIs, Dept. of Radiology and Biomedical Imaging, Yale School of Medicine.)