Bioimage QC Agent

Sat, 20 Jun 2026 00:00:00 -0500

Bioimage QC Agent is an interactive microscopy image segmentation and quality-control platform designed to improve the reliability and reproducibility of bioimage analysis workflows. The system integrates classical watershed segmentation, Cellpose deep-learning models, and the Segment Anything Model (SAM / micro-SAM) with an agentic quality-control framework that automatically detects segmentation failures and recommends corrective actions.

The platform follows an observe → decide → act → evaluate loop. Segmentation outputs are analyzed using image-quality metrics, object statistics, and benchmarking measures to identify over-segmentation, under-segmentation, low contrast, blur, and other common failure modes. When issues are detected, the QC agent recommends parameter adjustments and can automatically rerun segmentation to improve results.

A complementary Vision Transformer (ViT)-based quality-control classifier provides a learned alternative to rule-based QC assessment, enabling automated image-quality prediction without requiring manually annotated QC datasets.

Bioimage QC Agent supports:

Watershed-based nuclei segmentation
Cellpose deep-learning segmentation
Segment Anything Model (SAM) and micro-SAM segmentation
Automated segmentation benchmarking (Dice, IoU, object counts)
Rule-based quality-control assessment
ViT-based QC classification
Agentic parameter correction and rerun optimization
Interactive visualization and reporting through a Streamlit dashboard

The platform was developed using the BBBC038 / 2018 Data Science Bowl nuclei segmentation benchmark dataset and demonstrates practical agentic AI for biomedical image analysis.

The web dashboard allows users to:

Upload fluorescence or brightfield microscopy images
Interactively tune segmentation parameters
Compare raw images, masks, overlays, and object statistics
Inspect QC metrics and segmentation performance
View agent recommendations and automatic corrections
Download masks, overlays, metrics, and QC reports

Open Tool

Microscopy | Shovito Barua Soumma

Bioimage QC Agent