GT Checklist

Points to confirm while segmenting Ground Truth volumes, before marking a task complete.

• Use one segment for all extracellular space.
• Use one segment for objects that connect 20 slices outside the boundaries.
• Give parallel-plane boundaries the area they need — be careful not to overcolor them, and leave space for the boundary.
• When segmenting thin lines of glia or extracellular space, it's okay to bend the parallel-boundary rule and segment slightly darker-than-normal areas, so long as you believe they are part of those objects.
• Be cognizant of invaginations, and be careful of internal objects such as organelles / ER — always use a keen eye when investigating them.
• Watch the borders of your volume and check for small segments that just barely pass by; these are important and should be segmented.
• Myelin should be its own segment.

Dust, defects & fat globules

• If dust/defects are (nearly) fully contained within a single cell, color over them.
• If dust/defects span multiple cells:
  • if small enough that it's easy to draw an imaginary boundary between the involved cells, do so;
  • if too large for that, create a separate defect mask that can safely cover the dust or defects.
• For fat globules (or ER-membrane swirling, whichever applies), color them separately and as accurately as possible.

Always check with the project leader when you have questions, and keep a collection of images to illustrate tough areas you want clarified. These rules change — ask for help when you aren't sure.