Architecture Notes

Things worth knowing before changing the analysis pipeline.

fixed_seed_position vs. current_root_base

Both start as copies of the same manually-configured seed position.

• fixed_seed_position never changes for the rest of analysis.
• current_root_base gets reassigned every successfully-tracked frame, so it can drift over time.

Root component selection anchors on current_root_base (it should track legitimate drift). Hypocotyl selection anchors on fixed_seed_position, so it stays independent of any root-tracking mistakes and consistent frame-to-frame.

Main / Lateral Classification Is Topology-Based, Not Per-Pixel

graphInit() marks the longest weighted path from the seed as root_type=10 (main); everything else defaults to lateral. The skeleton is built from a merged binary mask (classes 1+2 combined) before any per-pixel class matters, so per-pixel main/lateral mislabeling in the segmentation mask does not corrupt MainRootLength / LateralRootsLength. It only affects the SegMulti visualization coloring used for human QC.

SegMulti Images Are Visualizations, Not Raw Masks

BGR color key:

Class	Color (BGR)	Grayscale value
Main root	(0,0,255) red	76
Lateral root	(0,255,0) green	150
Hypocotyl	(0,255,255) yellow	179
FTip marker	(255,255,0) cyan	226

The real multi-class mask (pixel values 0–7) lives at the path in each plant’s metadata.json under the SegPath key, e.g. <video>/Segmentation/Ensemble/.

Class Labels (dataset.json)

0 = background
1 = main root
2 = lateral root
3 = seed
4 = hypocotyl   (spelled "hypocotil": typo, preserved for compatibility)
5 = leaf
6 = petiole
7 = ignore

Case Naming

The live dataset and corrected_to_nnunet_cases.py / CreateArabidopsisDataset.ipynb use image_N, not CaseN. If you see CaseN anywhere, it’s stale; reconcile it.

What’s Different from Upstream ChronoRoot2

• chronoRootApp (upstream name) was renamed to singlePlantAnalysis here.
• imageAligner exists only in this fork, not upstream.
• Upstream has a chronoRootScreeningApp; this fork does not.