Learning to count small and clustered objects with application to bacterial colonies

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.

Counting living cells is an important step in many biological research workflows. Our collaborators at the Wellcome Sanger Institute study vital genes in humans via large scale saturation genome editing screening, which requires repeatedly counting cells a great number of times. Computer Vision based automation is crucial for high throughput and resource efficiency. In this work, we develop a regression-based deep learning computer vision algorithm to detect and count cells in phase-contrast microscopy images. To reduce annotation effort, which in practice often becomes a bottleneck, we focus on counting cells only using sparse point annotations, which are fast and easy to acquire. By comparison to state-of-the-art 0-shot methods, we show that regression-based counting is a promising alternative in low data regimes. Through developing methods to automatically count living cells in microscopy images, we contribute to valuable research on the human genome. The code is available at https://github.com/beijn/cellnet.

Object counting remains fragmented across domain-specific datasets and task formulations, despite rapid progress in generalist vision models. Existing counting models are often tailored to scenarios such as crowds, vehicles, cells, crops, or remote-sensing objects, and thus struggle to generalize across categories, visual domains, object scales, and density distributions. In this paper, we study text-guided object counting across domains, where a model takes an image and a natural-language query as input and returns an instance-grounded set of target points whose cardinality gives the count. This formulation unifies category-conditioned counting with interpretable spatial localization. To support this setting, we construct CLOC, a Cross-domain Large-scale Object Counting dataset that reorganizes diverse public data sources into a unified benchmark. CLOC covers six visual domains: General Scene, Remote Sensing, Histopathology, Cellular Microscopy, Agriculture, and Microbiology, with about 220K images, 619 categories, and 15M object instances. Based on CLOC, we propose Count Anything, a generalist model for text-guided object counting. Unlike density-map-based methods, which dominate counting models, Count Anything adopts discrete instance points and performs dual-granularity instance enumeration. A Region-level Sparse Counter provides object-level anchors for large and sparse targets, while a Pixel-level Dense Counter handles small, crowded, and weakly bounded targets via dense point prediction. A point-centric supervision strategy enables learning from heterogeneous annotations, and Complementary Count Fusion combines both counters in a parameter-free manner. Extensive experiments show that Count Anything achieves strong accuracy and multi-domain generalization, outperforming existing open-world counting methods. Code is available at: https://github.com/Mengqi-Lei/count-anything.