Image Quantification

The Image Quantification feature provides advanced tools for segmenting medical images directly in the SliceVault viewer. These tools allow users to outline regions of interest, apply segmentation labels, and generate quantitative outputs based on the study configuration.

Image quantification mode is accessed from the Visit Dashboard by clicking the Analyze button. This opens the viewer with the segmentation toolbar enabled, allowing annotation and quantification tasks as defined in the study protocol.

How to Segment Images

Once Analyze mode is opened, a segmentation menu becomes available in the viewer. From this menu, users can select labels, draw annotations, apply thresholds, adjust segmentation opacity, and upload segmentation results to the server.

Example – Manual Segmentation of CT Stack

Segmentation in SliceVault follows a straightforward workflow:

  1. Select a label from the segmentation menu.

    Note: Available segmentation labels are configured per study protocol.

  2. Draw the segmentation using the pencil, polygon tool, bucket fill, or threshold-based tools.

    The following auto-assistance tools help increase speed and precision:

    • Limit intensity
      Restricts segmentation to pixels within a chosen intensity range. Only pixels that fall inside the specified HU interval will be segmented, making it easier to isolate structures with characteristic intensities.

    • Fill holes
      Automatically fills interior gaps that are fully enclosed by labeled pixels. Useful for closing small gaps.

    • Clean
      Ensures that only pixels connected to the main labeled region gets labelled. Helps remove stray marks, speckles, or unintentional clicks.

    • Realtime
      Shows segmentation effects instantly while drawing. Particularly helpful with threshold tools, though it may increase device resource usage.

    Note: Each voxel can only have one segmentation label.

  3. Upload the segmentation to SliceVault to save your work.

All labels can be quantified, and SliceVault also provides a 3D model view of the segmentation for visual verification.

Using the segmentation tools requires a bit of practice, but the shortcuts below can dramatically improve segmentation speed.

Viewing Tools for Annotations

  • X – Toggle segmentation opacity (on/off)
  • ALT + scroll wheel – Manually adjust segmentation opacity
  • L – Show or hide all labels
  • Tab + mouse hover – Display label name when hovering over a segmentation
  • Numpad + / Numpad - – Cycle through available labels

Basic Drawing Tools

  • E + left mouse – Draw using pencil
  • E + right mouse – Erase using pencil
  • Q + left mouse – Erase using pencil
  • A – Increase pencil size
  • Z – Decrease pencil size
  • G + left mouse – Bucket fill
  • Ctrl + R + left mouse – Draw with polygon tool
  • J – Jump to current label
  • Ctrl + Z – Undo
  • Ctrl + Y – Redo
  • Ctrl + C – Copy segmentation from current slice
  • Ctrl + V – Paste segmentation to current slice
  • Ctrl + Alt + S – Upload segmentation to server

Advanced Drawing Tools

  • Y + scroll wheel – Set high HU threshold for pencil tool
  • H + scroll wheel – Set low HU threshold for pencil tool
  • Ctrl + H + left mouse – Set thresholds to intensities of marked area
  • Shift – Temporarily force basic pencil mode (ignores thresholds)
  • I – Remove marked pixels not part of the largest connected component (current slice)
  • D – Fill holes in the current label

Additional Resources

For general navigation, display controls, and viewer hotkeys, see:

DICOM Viewer

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