Colony Grounded SAM2: Zero-shot detection and segmentation of bacterial colonies using foundation models

Automatic bacterial colony counting is a highly sought-after technology in modern biological laboratories because it eliminates manual counting effort. Previous work has observed that MicrobiaNet, currently the best-performing cardinality classification model for colony counting, has difficulty distinguishing colonies of three or more individuals. However, it is unclear if this is due to properties of the data together with inherent characteristics of the MicrobiaNet model. By analysing MicrobiaNet with explainable artificial intelligence (XAI), we demonstrate that XAI can provide insights into how data properties constrain cardinality classification performance in colony counting. Our results show that high visual similarity across classes is the key issue hindering further performance improvement, revising prior assertions about MicrobiaNet. These findings suggest future work should focus on models that explicitly incorporate visual similarity or explore density estimation approaches, with broader implications for neural network classifiers trained on imbalanced datasets.

Automated bacterial colony counting from images is an important technique to obtain data required for the development of vaccines and antibiotics. However, bacterial colonies present unique machine vision challenges that affect counting, including (1) small physical size, (2) object clustering, (3) high data annotation cost, and (4) limited cross-species generalisation. While FamNet is an established object counting technique effective for clustered objects and costly data annotation, its effectiveness for small colony sizes and cross-species generalisation remains unknown. To address the first three challenges, we propose ACFamNet, an extension of FamNet that handles small and clustered objects using a novel region of interest pooling with alignment and optimised feature engineering. To address all four challenges above, we introduce ACFamNet Pro, which augments ACFamNet with multi-head attention and residual connections, enabling dynamic weighting of objects and improved gradient flow. Experiments show that ACFamNet Pro achieves a mean normalised absolute error (MNAE) of 9.64% under 5-fold cross-validation, outperforming ACFamNet and FamNet by 2.23% and 12.71%, respectively.

Bird image segmentation remains a challenging task in computer vision due to extreme pose diversity, complex plumage patterns, and variable lighting conditions. This paper presents a dual-pipeline framework for binary bird image segmentation leveraging 2025 foundation models. We introduce two operating modes built upon Segment Anything Model 2.1 (SAM 2.1) as a shared frozen backbone: (1) a zero-shot pipeline using Grounding DINO 1.5 to detect birds via the text prompt "bird" before prompting SAM 2.1 with bounding boxes requiring no labelled bird data; and (2) a supervised pipeline that fine-tunes YOLOv11 on the CUB-200-2011 dataset for high-precision detection, again prompting SAM 2.1 for pixel-level masks. The segmentation model is never retrained for new species or domains. On CUB-200-2011 (11,788 images, 200 species), the supervised pipeline achieves IoU 0.912, Dice 0.954, and F1 0.953 outperforming all prior baselines including SegFormer-B2 (IoU 0.842) by +7.0 percentage points. The zero-shot pipeline achieves IoU 0.831 using only a text prompt, the first such result reported on this benchmark. We demonstrate that prompt-based foundation model pipelines outperform task specific end-to-end trained segmentation networks, while requiring only lightweight detector fine-tuning (~1 hour) for domain adaptation. Complete PyTorch implementation, dataset preparation scripts, and trained weights are publicly available.