Imaging & vision

Root Image Preprocessor

Name: Root Image Preprocessor
Author: Liangchao Deng

RootQuantify in the browser: trace the root region, remove the background by morphological closing, threshold at full resolution and correct by hand.

Matches RootQuantify
Full resolution
PNG export

StableVersion 2026.10.2Validated 2026-10-14Same processing as the desktop RootQuantify (RootImager.py). On 403 test scans, up to 6000 × 8000 px, every pixel of the result, polygon mask included, matched RootQuantify run with OpenCV 4.14 and 5.0 (about 200 million pixels); the browser gave identical results for PNG and JPEG input.

Guide

RootQuantify in the browser: trace the root region, run its background subtraction and threshold at full resolution, then correct by hand.

Upload JPG/PNG scans of root systems to begin.

Original Preview

Read-only

ROI / Processing Canvas

Click to add polygon points

ROI Polygon

Click on the right canvas to trace the region containing the root system.

Points: 0Open

Automation

Runs RootQuantify's processing on the ROI: background by morphological closing, subtraction, min–max normalization and threshold. The result is the ROI rectangle with roots black on white, as the desktop tool saves it.

Manual Cleanup

After automation, switch to manual mode to adjust fine details with brush + undo.

Brush modeBrush size (11px)

Export

Cite this work

If you use the Digital Plant Phenotyping Platform v25.0 or any of its tools in your research, please cite it.

DOI10.5281/zenodo.17544584

APA

LiangchaoDeng. (2025). smiler488/smiler488.github.io: Digital Plant Phenotyping Platform v25.0 (v25.0.0). Zenodo. https://doi.org/10.5281/zenodo.17544584

BibTeX

@software{Deng2025_DPPP_v25,
  author       = {Deng, Liangchao},
  title        = {Digital Plant Phenotyping Platform (v25.0)},
  year         = {2025},
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.17544584},
  url          = {https://doi.org/10.5281/zenodo.17544584},
  note         = {[Computer software]}
}

In Zotero, open the File menu and choose Import from Clipboard.

Parameter record

Each export from this tool produces a record of the settings, tool version and file checksums, so the result can be reproduced later.

No export yet in this session.

Continue with

Tools that accept what this one produces.

Processing workspace