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Abstract—Accurate cell counting is essential in various biomedical research and clinical applications, including cancer diagnosis, stem cell research, and immunology. Manual counting is labor-intensive and error-prone, motivating automation through deep learning techniques. However, training reliable deep learning models requires large amounts of high-quality annotated data, which is difficult and time-consuming to produce manually. Consequently, existing cell-counting datasets are often limited, frequently containing fewer than 500 images. In this work, we introduce a large-scale annotated dataset comprising 3,023 images from immunocytochemistry experiments related to cellular differentiation, containing over 430,000 manually annotated cell locations. The dataset presents significant challenges: high cell density, overlapping and morphologically diverse cells, a long-tailed distribution of cell count per image, and variation in staining protocols. We benchmark three categories of existing methods: regression-based, crowd-counting, and cell-counting techniques on a test set with cell counts ranging from 10 to 2,126 cells per image. We also evaluate how the Segment Anything Model (SAM) can be adapted for microscopy cell counting using only dot-annotated datasets. As a case study, we implement a density-map-based adaptation of SAM (SAM-Counter) and report a mean absolute error (MAE) of 22.12, which outperforms existing approaches (second-best MAE of 27.46). Our results underscore the value of the dataset and the benchmarking framework for driving progress in automated cell counting and provide a robust foundation for future research and development.
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CountXplain: Interpretable Cell Counting with Prototype-Based Density Map Estimation
Cell counting in biomedical imaging is pivotal for various clinical applications, yet the interpretability of deep learning models in this domain remains a signifcant challenge. We propose a novel prototype-based method for interpretable cell counting via density map estimation. Our approach integrates a prototype layer into the density estimation network, enabling the model to learn representative visual patterns for both cells and background artifacts. The learned prototypes were evaluated through a survey of biologists, who confirmed the relevance of the visual patterns identified, further validating the interpretability of the model. By generating interpretations that highlight regions in the input image most similar to each prototype, our method offers a clear understanding of how the model identifies and counts cells. Extensive experiments on two public datasets demonstrate that the tour method achieves interpretability without compromising counting effectiveness. This work provides researchers and clinicians with a transparent and reliable tool for cell counting, potentially increasing trust and accelerating the adoption of deep learning in critical biomedical applications. Code is available at https://github.com/NRT-D4/CountXplain. Keywords: Cell Counting, Biomedical Imaging, Deep Learning, Interpretability, Density, Map Estimation
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- Award ID(s):
- 2152117
- PAR ID:
- 10678705
- Publisher / Repository:
- Openreview.net
- Date Published:
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Abstract—Generating realistic synthetic microscopy images is critical for training deep learning models in label-scarce environments, such as cell counting with many cells per image. However, traditional domain adaptation methods often struggle to bridge the domain gap when synthetic images lack the complex textures and visual patterns of real samples. In this work, we adapt the Inversion-Based Style Transfer (InST) framework originally designed for artistic style transfer to biomedical microscopy images. Our method combines latent-space Adaptive Instance Normalization with stochastic inversion in a diffusion model to transfer the style from real fuorescence microscopy images to synthetic ones, while weakly preserving content structure. We evaluate the effectiveness of our InST-based synthetic dataset for downstream cell counting by pre-training and fne tuning EffcientNet-B0 models on various data sources, including real data, hard-coded synthetic data, and the public Cell200-s dataset. Models trained with our InST-synthesized images achieve up to 37% lower Mean Absolute Error (MAE) compared to models trained on hard-coded synthetic data, and a 52% reduction in MAE compared to models trained on Cell200-s (from 53.70 to 25.95 MAE). Notably, our approach also outperforms models trained on real data alone (25.95 vs. 27.74 MAE). Further improvements are achieved when combining InST-synthesized data with lightweight domain adaptation techniques such as DACS with CutMix. These findings demonstrate that InST-based style transfer most effectively reduces the domain gap between synthetic and real microscopy data. Our approach offers a scalable path for enhancing cell counting performance while minimizing manual labeling effort. The source code and resources are publicly available at: https://github.com/MohammadDehghan/ InST-Microscopymore » « less
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Stereology-based methods provide the current state-of-the-art approaches for accurate quantification of numbers and other morphometric parameters of biological objects in stained tissue sections. The advent of artificial intelligence (AI)-based deep learning (DL) offers the possibility of improving throughput by automating the collection of stereology data. We have recently shown that DL can effectively achieve comparable accuracy to manual stereology but with higher repeatability, improved throughput, and less variation due to human factors by quantifying the total number of immunostained cells at their maximal profile of focus in extended depth of field (EDF) images. In the first of two novel contributions in this work, we propose a semi-automatic approach using a handcrafted Adaptive Segmentation Algorithm (ASA) to automatically generate ground truth on EDF images for training our deep learning (DL) models to automatically count cells using unbiased stereology methods. This update increases the amount of training data, thereby improving the accuracy and efficiency of automatic cell counting methods, without a requirement for extra expert time. The second contribution of this work is a Multi-channel Input and Multi-channel Output (MIMO) method using a U-Net deep learning architecture for automatic cell counting in a stack of z-axis images (also known as disector stacks). This DL-based digital automation of the ordinary optical fractionator ensures accurate counts through spatial separation of stained cells in the z-plane, thereby avoiding false negatives from overlapping cells in EDF images without the shortcomings of 3D and recurrent DL models. The contribution overcomes the issue of under-counting errors with EDF images due to overlapping cells in the z-plane (masking). We demonstrate the practical applications of these advances with automatic disector-based estimates of the total number of NeuN-immunostained neurons in a mouse neocortex. In summary, this work provides the first demonstration of automatic estimation of a total cell number in tissue sections using a combination of deep learning and the disector-based optical fractionator method.more » « less
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null (Ed.)Abstract The development of single-cell methods for capturing different data modalities including imaging and sequencing has revolutionized our ability to identify heterogeneous cell states. Different data modalities provide different perspectives on a population of cells, and their integration is critical for studying cellular heterogeneity and its function. While various methods have been proposed to integrate different sequencing data modalities, coupling imaging and sequencing has been an open challenge. We here present an approach for integrating vastly different modalities by learning a probabilistic coupling between the different data modalities using autoencoders to map to a shared latent space. We validate this approach by integrating single-cell RNA-seq and chromatin images to identify distinct subpopulations of human naive CD4+ T-cells that are poised for activation. Collectively, our approach provides a framework to integrate and translate between data modalities that cannot yet be measured within the same cell for diverse applications in biomedical discovery.more » « less
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