NPEC — research (in progress) Publication
4-Channel RT-DETR for Overlapping Roots
Research in progress
Ongoing research tackling a known blind spot in high-throughput phenotyping: current frameworks discard any image with touching or overlapping plants. I'm testing whether encoding root-intersection points as a spatial topological prior in a 4-channel RT-DETR can recover that lost data.
Context
This is the next phase of my root phenotyping work for NPEC, and it is actively in progress. The earlier system assumed roots don’t overlap — a fair assumption early in an experiment, but one that breaks down fast.
The gap
State-of-the-art phenotyping frameworks are excellent at automating analysis, but in high-throughput mode they discard every image containing at least one touching or overlapping plant. For Arabidopsis thaliana, plants begin overlapping around day 30 — and experiments often run 50–60 days — so a large, valuable slice of the data is simply thrown away.
The core difficulty is optical: at a root-crossing point, the RGB values and root widths are almost identical to ordinary, un-entangled root, so a standard detector has nothing obvious to separate one plant from another.
Research question
How does integrating a spatial topological layer — encoding root-intersection points as geometric priors — affect the mean Average Precision (mAP) of an RT-DETR model when identifying individual plants in high-density Petri dishes with moderate-to-heavy root crossing?
Status
Currently in the research phase: preliminary exploratory analysis is done, the gap is characterised against existing frameworks, and the experimental design around the 4-channel RT-DETR approach is underway. Results and a write-up will follow — this card will be updated as the work progresses.