Object Counting

Analyzing microscopy images to extract biological object properties (e.g., their morphological organization, temporal dynamics, and population density) is fundamental to various biomedical research. Yet conducting this manually is costly and time-consuming. Though deep learning-based approaches have been explored to automate this process, the substantial diversity of microscopy analysis settings in practice (including variations of biological object types, sample processing protocols, imaging equipment, and analysis tasks, etc.) often renders them ineffective. As a result, these approaches typically require extensive adaptation for different settings, which, however, can impose burdens that are often practically unsustainable for laboratories, forcing biomedical researchers to still commonly rely on manual analysis, thereby severely bottlenecking the pace of biomedical research progress. This situation has created a pressing and long-standing need for a reliable and broadly applicable microscopy image analysis tool, yet such a tool is still missing. To address this gap, we present the first ready-to-use microscopy image analysis framework, MicroscopyMatching, that can reliably perform key analysis tasks (including segmentation, tracking, and counting) across diverse microscopy analysis settings. From a fundamentally different perspective, MicroscopyMatching reformulates diverse microscopy image analysis tasks as a unified matching problem, effectively handling this problem by exploiting the robust matching capability from pre-trained latent diffusion models.

Open-world object counting remains brittle: despite rapid advances in vision-language models (VLMs), reliably counting the objects a user intends is far from solved. We argue that a central reason is that counting granularity is left implicit; users may refer to a specific identity, an attribute, an instance type, a category, or an abstract concept, yet most methods treat "what to count" as a single, category-level matching problem. In this work, we redefine open-world counting as multi-grained counting, where visual exemplars specify target appearance and fine-grained text, with optional negative prompts, specifies the intended semantic granularity across five explicit levels. Making granularity explicit, however, exposes a critical data bottleneck: existing counting datasets lack the multi-category scenes, controlled distractors, and instance-level annotations needed to verify fine-grained prompt semantics. To address this, we propose the first fully automatic data-scaling pipeline that integrates controllable 3D synthesis with consistent image editing and VLM-based filtering, and use it to construct KubriCount, the largest and most comprehensively annotated counting dataset to date, supporting both training and multi-grained evaluation. Systematic benchmarking reveals that both multimodal large language models and specialist counting models exhibit severe prompt-following failures under fine-grained distinctions. Motivated by these findings, we train HieraCount, a multi-grained counting model that jointly leverages text and visual exemplars as complementary target specifications. HieraCount substantially improves multi-grained counting accuracy and generalizes robustly to challenging real-world scenarios. The project page is available here: https://verg-avesta.github.io/KubriCount/.

Large language models often fail at simple counting tasks, even when items to count are in the prompt. We investigate whether this failure occurs because transformers do not represent counts internally, or because they cannot convert representations to the correct output tokens. Across three model families: Pythia, Qwen3, and Mistral, ranging from 0.4B to 14B parameters, we find evidence for the second explanation. Linear probes recover the correct count from intermediate layers with $R^2>0.99$, showing that the information is present. However, the internal directions that encode counts are nearly orthogonal to digit-token output-head rows ($|\cos| \leq 0.032$). In other words, the model stores the count in a form that the digit logits do not naturally read out. We localize this failure with two interventions. Updating only the digit rows of the output head (36,864 parameters) substantially improves constrained digit prediction (60.7--100.0% on four tasks), but it does not fix unconstrained generation (0%); we do not claim that digit-row repair fixes open-ended text. By contrast, small LoRA on attention Q/V (7.67M parameters) improves upstream routing and achieves 83.1%$\pm$7.2% in true greedy autoregressive generation (deployable fix). Logit-lens at layer 35 (entity counting; correct-digit rank): (i) median over 3 seeds drops from order-$10^4$ to 1; (ii) seed 42 shows $54{,}332 \to 838$ (median top-1 while one seed stays far below). Norm, logit-lens, and cross-task analyses generalize the bottleneck to counting, addition, and list length; nulls on MMLU and GSM8K and limited DROP transfer. These results identify counting failure as a geometric readout bottleneck, not an internal-representation failure: the model knows the count but the output pathway is misaligned with tokens needed to express it.

Open-world text-guided class-agnostic counting (CAC) has emerged as a flexible paradigm for counting arbitrary object classes by using natural language prompts. However, current evaluation protocols primarily focus on standard counting errors within single-category images, overlooking a fundamental requirement: the ability to correctly ground the textual prompt in the visual scene. In this paper, we show that several state-of-the-art CAC models often struggle to determine which object class should be counted based on the given prompt, revealing a misalignment between textual semantics and visual object representations. This limitation leads to spurious counting responses and reduced reliability in real-world scenarios. To systematically address these limitations, we propose a new evaluation framework focused on model robustness and trustworthiness. Our contribution is two-fold: (i) we introduce PrACo++ (Prompt-Aware Counting++), a novel test suite featuring two dedicated evaluation protocols -- the negative-label test and the distractor test -- paired with new specialized metrics; and (ii) we present the MUCCA (MUlti-Category Class-Agnostic counting) evaluation dataset, a new collection of real-world images featuring multiple annotated object categories per scene, unlike existing CAC benchmarks that typically include a single category per image. Our extensive experimental evaluation of 10 state-of-the-art methods shows that, despite strong performance under standard counting metrics, current models exhibit significant weaknesses in understanding and grounding object class descriptions. Finally, we provide a quantitative analysis of how semantic similarity between prompts influences these failures. Overall, our results underscore the need for more semantically grounded architectures and offer a reliable framework for future assessment in open-world text-guided CAC methods.

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.

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.

Video understanding requires models to continuously track and update world state during playback. Although existing benchmarks have advanced video understanding evaluation across multiple dimensions, they provide limited visibility into how models maintain world state over time. We propose SVCBench, a Streaming Video Counting Benchmark that repositions counting as a minimal, controlled probe for diagnosing models' world-state maintenance capability. We decompose this capability into object counting and event counting, forming 8 fine-grained subcategories. Object counting covers tracking currently visible objects and cumulative unique identities, while event counting covers detecting instantaneous actions and tracking complete activity cycles. SVCBench contains 406 videos with frame-by-frame annotations of 10,071 event occurrences and object state changes, yielding 1,000 streaming QA pairs with 4,576 query points distributed along video timelines. By observing state maintenance trajectories through streaming multi-point queries, we design three complementary metrics to diagnose numerical precision, trajectory consistency, and temporal awareness. Evaluations of mainstream video-language models show that current models still exhibit significant deficiencies in spatial-temporal state maintenance, with especially poor performance on periodic event counting. SVCBench provides a diagnostic framework for measuring and improving state maintenance in video understanding systems. Our code and data are available at https://buaa-colalab.github.io/SVCBench.

Low-shot object counting addresses estimating the number of previously unobserved objects in an image using only few or no annotated test-time exemplars. A considerable challenge for modern low-shot counters are dense regions with small objects. While total counts in such situations are typically well addressed by density-based counters, their usefulness is limited by poor localization capabilities. This is better addressed by point-detection-based counters, which are based on query-based detectors. However, due to limited number of pre-trained queries, they underperform on images with very large numbers of objects, and resort to ad-hoc techniques like upsampling and tiling. We propose CoDi, the first latent diffusion-based low-shot counter that produces high-quality density maps on which object locations can be determined by non-maxima suppression. Our core contribution is the new exemplar-based conditioning module that extracts and adjusts the object prototypes to the intermediate layers of the denoising network, leading to accurate object location estimation. On FSC benchmark, CoDi outperforms state-of-the-art by 15% MAE, 13% MAE and 10% MAE in the few-shot, one-shot, and reference-less scenarios, respectively, and sets a new state-of-the-art on MCAC benchmark by outperforming the top method by 38% MAE. The code is available at https://github.com/gsustar/CoDi

Diffusion models excel at photorealistic synthesis but struggle with object count fidelity, especially in high-density settings. We introduce COUNTLOOP, a training-free framework that achieves structured instance and count control through iterative, structured feedback. Our method alternates between synthesis and evaluation: a VLM-based planner generates structured scene layouts, while a VLM-based critic provides explicit feedback on object counts, spatial arrangements, and visual quality to refine the layout iteratively. Instance-driven attention masking and cumulative attention composition further prevent semantic leakage, ensuring clear object separation even in densely occluded scenes. Evaluations on COCO-Count, T2I-CompBench, and two newly introduced high instance benchmarks show that COUNTLOOP reduces counting error by up to 57% and achieves the highest or comparable spatial quality scores across all benchmarks, while maintaining photorealism. Project page is at https://mondalanindya.github.io/CountLoop/.

We present ABACUS, a unified vision-language model that jointly addresses object counting, crowd counting, referring-expression counting, and count-faithful image generation within a single 3B-parameter model. ABACUS introduces three contributions: density-aware adaptive zooming paired with an objectness map from multi-head self-attention decomposition to spatially ground count predictions; a boundary-aware count policy trained via GRPO with nested local, boundary, and global rewards to eliminate over- and undercounting at crop boundaries; and a cycle-consistent GRPO strategy in which the frozen understanding branch scores generated candidates on count-deviation and aesthetic quality, closing the understanding-generation synergy gap without any external critic or annotation. ABACUS achieves state-of-the-art results across seven benchmarks spanning object counting (FSC-147, CARPK), crowd counting (ShanghaiTech A/B), referring-expression counting (REC-8K), count-faithful generation (CoCoCount, T2I-CompBench, GenEval), and count reasoning (CountQA), surpassing both task-specific specialists and larger generalist models. Project page is at https://mondalanindya.github.io/pages/ABACUS.