Simple Color vs Terminology Color usage

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Hi, James.
As you’ve invited my comment I can let you know my current practice, whilst you keep in mind that it may not be optimal and may not represent the majority of users…

Foremost I care about the colours of the individual segments of a segmentation, and in this there are a few priorities:

  1. To readily distinguish one segment from another. Here I would be more-or-less in line with your earlier statement (quoted below).
  1. To provide distinction between a segment and another ‘overlaid’ object. In the 3D viewing port that would most commonly be a 3D rendering of the volume, but could also be an object imported into the Data structure from an STL file (e.g. somebody else’s earlier attempt at a segmentation of the same feature); also control points from the Markups module (mostly Fiducial markers). In the 2D slice viewers of course it would be the DICOM series (which are typically CT scans, which I view in greyscale).
  2. To allow clear visualisation of surface morphology in the 3D view: some colours seem to me to have more obvious shadows.

Besides all of that, I might try to organise colours thematically: let’s say red, orange and pink for objects imported as STLs, and blue, cyan and green for segments.

I don’t use terminologies, as

  • the audience is generally me;
  • I don’t segment lots of different types of features (I’m not trying to build an atlas);
  • I am mainly interested in segmenting one main type of feature (brain aneurysms, with a shortish length of connected arteries).

Furthermore — and this may not be an obvious workflow, so I describe it here in some detail — I may have multiple segments for one single feature.

For example (1), I might …

  • create a preliminary segment based on thresholding;
  • make a copy of that segment and smooth it by one method;
  • make a further copy of the original segment and smooth it by a different method; and
  • compare the three segments to identify the impact of each smoothing effect and choose the ‘best’ one.

For example (2), I might …

  • create a preliminary segment;
  • make a copy of that segment and use the Scissors, Erase, Paint and/or Draw effects to ‘manually’ add/remove voxels;
  • I can compare the two segments to see the impact of my changes; and
  • if at some later stage I decide that the changes weren’t quite right, then the preliminary segment is still available to try again.

For example (3), I might …

  • segment the feature using a Threshold effect;
  • segment the same feature (from scratch) using a Grow from seeds effect;
  • compare the two segments, and choose the ‘best’ one to export.

Hope this helps,
DIV

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