Wallapak Tavanapong

Mohammad Dehghanmanshadi, Wallapak Tavanapong

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 fluorescence 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 fine-tuning EfficientNet-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-Microscopy.

Seok Hwan Song, Azher Ahmed Efat, Wallapak Tavanapong

Chart-to-table translation converts chart images into structured tabular data. Accurate translation is crucial for Multimodal Language Model (MLM) to answer complex queries. We observe imbalances in the number of images across different aspects of the y-axis information in public chart datasets. Such imbalances can introduce unintended biases, causing uneven MLM performance. Previous works have not systematically examined these biases. To address this gap, we propose a new framework, FairChart2Table, for analyzing y-axis-related bias on five state-of-the-art models. Key Findings: (1) There are significant y-axis biases related to the digit length of the major tick values, the number of major ticks, the range of values, and the tick value format (e.g., abbreviation or scientific format). (2) The number of legends/entities in chart images impacts MLM performance. (3) Prompting MLM with y-axis information can significantly enhance the performance for some MLMs.

Azher Ahmed Efat, Seok Hwan Song, Wallapak Tavanapong

Charts are widely used to present complex information. Deriving meaningful insights in real-world contexts often requires interpreting multiple related charts together. Research on understanding multi-chart images has not been extensively explored. We introduce PolyChartQA, a mid-scale dataset specifically designed for question answering over multi-chart images. PolyChartQA comprises 534 multi-chart images (with a total of 2,297 sub-charts) sourced from peer-reviewed computer science research publications and 2,694 QA pairs. We evaluate the performance of nine state-of-the-art Multimodal Language Models (MLMs) on PolyChartQA across question type, difficulty, question source, and key structural characteristics of multi-charts. Our results show a 27.4% LLM-based accuracy (L-Accuracy) drop on human-authored questions compared to MLM-generated questions, and a 5.39% L-accuracy gain with our proposed prompting method.

Abdurahman Ali Mohammed, Wallapak Tavanapong, Catherine Fonder et al.

Cell counting in biomedical imaging is pivotal for various clinical applications, yet the interpretability of deep learning models in this domain remains a significant 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 our 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.

Seok Hwan Song, Mohna Chakraborty, Qi Li et al.

Large Language Models (LLMs) have been evaluated using diverse question types, e.g., multiple-choice, true/false, and short/long answers. This study answers an unexplored question about the impact of different question types on LLM accuracy on reasoning tasks. We investigate the performance of five LLMs on three different types of questions using quantitative and deductive reasoning tasks. The performance metrics include accuracy in the reasoning steps and choosing the final answer. Key Findings: (1) Significant differences exist in LLM performance across different question types. (2) Reasoning accuracy does not necessarily correlate with the final selection accuracy. (3) The number of options and the choice of words, influence LLM performance.

Abdurahman Ali Mohammed, Catherine Fonder, Donald S. Sakaguchi et al.

We present a new annotated microscopic cellular image dataset to improve the effectiveness of machine learning methods for cellular image analysis. Cell counting is an important step in cell analysis. Typically, domain experts manually count cells in a microscopic image. Automated cell counting can potentially eliminate this tedious, time-consuming process. However, a good, labeled dataset is required for training an accurate machine learning model. Our dataset includes microscopic images of cells, and for each image, the cell count and the location of individual cells. The data were collected as part of an ongoing study investigating the potential of electrical stimulation to modulate stem cell differentiation and possible applications for neural repair. Compared to existing publicly available datasets, our dataset has more images of cells stained with more variety of antibodies (protein components of immune responses against invaders) typically used for cell analysis. The experimental results on this dataset indicate that none of the five existing models under this study are able to achieve sufficiently accurate count to replace the manual methods. The dataset is available at https://figshare.com/articles/dataset/Dataset/21970604.

Abdurahman Ali Mohammed, Catherine Fonder, Ying Wei et al.

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.