Deep Learning Enabled Segmentation, Classification and Risk Assessment of Cervical Cancer

Cervical cancer, the fourth leading cause of cancer in women globally, requires early detection through Pap smear tests to identify precancerous changes and prevent disease progression. In this study, we performed a focused analysis by segmenting the cellular boundaries and drawing bounding boxes to isolate the cancer cells. A novel Deep Learning (DL) architecture, the ``Multi-Resolution Fusion Deep Convolutional Network", was proposed to effectively handle images with varying resolutions and aspect ratios, with its efficacy showcased using the SIPaKMeD dataset. The performance of this DL model was observed to be similar to the state-of-the-art models, with accuracy variations of a mere 2\% to 3\%, achieved using just 1.7 million learnable parameters, which is approximately 85 times less than the VGG-19 model. Furthermore, we introduced a multi-task learning technique that simultaneously performs segmentation and classification tasks and begets an Intersection over Union score of 0.83 and a classification accuracy of 90\%. The final stage of the workflow employs a probabilistic approach for risk assessment, extracting feature vectors to predict the likelihood of normal cells progressing to malignant states, which can be utilized for the prognosis of cervical cancer.

Machine Learning Derived Blood Input for Dynamic PET Images of Rat Heart

Dynamic FDG PET imaging study of n = 52 rats including 26 control Wistar-Kyoto (WKY) rats and 26 experimental spontaneously hypertensive rats (SHR) were performed using a Siemens microPET and Albira trimodal scanner longitudinally at 1, 2, 3, 5, 9, 12 and 18 months of age. A 15-parameter dual output model correcting for spill over contamination and partial volume effects with peak fitting cost functions was developed for simultaneous estimation of model corrected blood input function (MCIF) and kinetic rate constants for dynamic FDG PET images of rat heart in vivo. Major drawbacks of this model are its dependence on manual annotations for the Image Derived Input Function (IDIF) and manual determination of crucial model parameters to compute MCIF. To overcome these limitations, we performed semi-automated segmentation and then formulated a Long-Short-Term Memory (LSTM) cell network to train and predict MCIF in test data using a concatenation of IDIFs and myocardial inputs and compared them with reference-modeled MCIF. Thresholding along 2D plane slices with two thresholds, with T1 representing high-intensity myocardium, and T2 representing lower-intensity rings, was used to segment the area of the LV blood pool. The resultant IDIF and myocardial TACs were used to compute the corresponding reference (model) MCIF for all data sets. The segmented IDIF and the myocardium formed the input for the LSTM network. A k-fold cross validation structure with a 33:8:11 split and 5 folds was utilized to create the model and evaluate the performance of the LSTM network for all datasets. To overcome the sparseness of data as time steps increase, midpoint interpolation was utilized to increase the density of datapoints beyond time = 10 minutes. The model utilizing midpoint interpolation was able to achieve a 56.4% improvement over previous Mean Squared Error (MSE).

Automated Quality Evaluation of Cervical Cytopathology Whole Slide Images Based on Content Analysis

The ThinPrep Cytologic Test (TCT) is the most widely used method for cervical cancer screening, and the sample quality directly impacts the accuracy of the diagnosis. Traditional manual evaluation methods rely on the observation of pathologist under microscopes. These methods exhibit high subjectivity, high cost, long duration, and low reliability. With the development of computer-aided diagnosis (CAD), an automated quality assessment system that performs at the level of a professional pathologist is necessary. To address this need, we propose a fully automated quality assessment method for Cervical Cytopathology Whole Slide Images (WSIs) based on The Bethesda System (TBS) diagnostic standards, artificial intelligence algorithms, and the characteristics of clinical data. The method analysis the context of WSIs to quantify quality evaluation metrics which are focused by TBS such as staining quality, cell counts and cell mass proportion through multiple models including object detection, classification and segmentation. Subsequently, the XGBoost model is used to mine the attention paid by pathologists to different quality evaluation metrics when evaluating samples, thereby obtaining a comprehensive WSI sample score calculation model. Experimental results on 100 WSIs demonstrate that the proposed evaluation method has significant advantages in terms of speed and consistency.

Pretrained hybrid transformer for generalizable cardiac substructures segmentation from contrast and non-contrast CTs in lung and breast cancers

AI automated segmentations for radiation treatment planning (RTP) can deteriorate when applied in clinical cases with different characteristics than training dataset. Hence, we refined a pretrained transformer into a hybrid transformer convolutional network (HTN) to segment cardiac substructures lung and breast cancer patients acquired with varying imaging contrasts and patient scan positions. Cohort I, consisting of 56 contrast-enhanced (CECT) and 124 non-contrast CT (NCCT) scans from patients with non-small cell lung cancers acquired in supine position, was used to create oracle with all 180 training cases and balanced (CECT: 32, NCCT: 32 training) HTN models. Models were evaluated on a held-out validation set of 60 cohort I patients and 66 patients with breast cancer from cohort II acquired in supine (n=45) and prone (n=21) positions. Accuracy was measured using DSC, HD95, and dose metrics. Publicly available TotalSegmentator served as the benchmark. The oracle and balanced models were similarly accurate (DSC Cohort I: 0.80 \pm 0.10 versus 0.81 \pm 0.10; Cohort II: 0.77 \pm 0.13 versus 0.80 \pm 0.12), outperforming TotalSegmentator. The balanced model, using half the training cases as oracle, produced similar dose metrics as manual delineations for all cardiac substructures. This model was robust to CT contrast in 6 out of 8 substructures and patient scan position variations in 5 out of 8 substructures and showed low correlations of accuracy to patient size and age. A HTN demonstrated robustly accurate (geometric and dose metrics) cardiac substructures segmentation from CTs with varying imaging and patient characteristics, one key requirement for clinical use. Moreover, the model combining pretraining with balanced distribution of NCCT and CECT scans was able to provide reliably accurate segmentations under varied conditions with far fewer labeled datasets compared to an oracle model.

GNCAF: A GNN-based Neighboring Context Aggregation Framework for Tertiary Lymphoid Structures Semantic Segmentation in WSI

Tertiary lymphoid structures (TLS) are organized clusters of immune cells, whose maturity and area can be quantified in whole slide image (WSI) for various prognostic tasks. Existing methods for assessing these characteristics typically rely on cell proxy tasks and require additional post-processing steps. In this work, We focus on a novel task-TLS Semantic Segmentation (TLS-SS)-which segments both the regions and maturation stages of TLS in WSI in an end-to-end manner. Due to the extensive scale of WSI and patch-based segmentation strategies, TLS-SS necessitates integrating from neighboring patches to guide target patch (target) segmentation. Previous techniques often employ on multi-resolution approaches, constraining the capacity to leverage the broader neighboring context while tend to preserve coarse-grained information. To address this, we propose a GNN-based Neighboring Context Aggregation Framework (GNCAF), which progressively aggregates multi-hop neighboring context from the target and employs a self-attention mechanism to guide the segmentation of the target. GNCAF can be integrated with various segmentation models to enhance their ability to perceive contextual information outside of the patch. We build two TLS-SS datasets, called TCGA-COAD and INHOUSE-PAAD, and make the former (comprising 225 WSIs and 5041 TLSs) publicly available. Experiments on these datasets demonstrate the superiority of GNCAF, achieving a maximum of 22.08% and 26.57% improvement in mF1 and mIoU, respectively. Additionally, we also validate the task scalability of GNCAF on segmentation of lymph node metastases.

Reinforced Correlation Between Vision and Language for Precise Medical AI Assistant

Medical AI assistants support doctors in disease diagnosis, medical image analysis, and report generation. However, they still face significant challenges in clinical use, including limited accuracy with multimodal content and insufficient validation in real-world settings. We propose RCMed, a full-stack AI assistant that improves multimodal alignment in both input and output, enabling precise anatomical delineation, accurate localization, and reliable diagnosis through hierarchical vision-language grounding. A self-reinforcing correlation mechanism allows visual features to inform language context, while language semantics guide pixel-wise attention, forming a closed loop that refines both modalities. This correlation is enhanced by a color region description strategy, translating anatomical structures into semantically rich text to learn shape-location-text relationships across scales. Trained on 20 million image-mask-description triplets, RCMed achieves state-of-the-art precision in contextualizing irregular lesions and subtle anatomical boundaries, excelling in 165 clinical tasks across 9 modalities. It achieved a 23.5% relative improvement in cell segmentation from microscopy images over prior methods. RCMed's strong vision-language alignment enables exceptional generalization, with state-of-the-art performance in external validation across 20 clinically significant cancer types, including novel tasks. This work demonstrates how integrated multimodal models capture fine-grained patterns, enabling human-level interpretation in complex scenarios and advancing human-centric AI healthcare.

AI-Driven Segmentation and Analysis of Microbial Cells

Studying the growth and metabolism of microbes provides critical insights into their evolutionary adaptations to harsh environments, which are essential for microbial research and biotechnology applications. In this study, we developed an AI-driven image analysis system to efficiently segment individual cells and quantitatively analyze key cellular features. This system is comprised of four main modules. First, a denoising algorithm enhances contrast and suppresses noise while preserving fine cellular details. Second, the Segment Anything Model (SAM) enables accurate, zero-shot segmentation of cells without additional training. Third, post-processing is applied to refine segmentation results by removing over-segmented masks. Finally, quantitative analysis algorithms extract essential cellular features, including average intensity, length, width, and volume. The results show that denoising and post-processing significantly improved the segmentation accuracy of SAM in this new domain. Without human annotations, the AI-driven pipeline automatically and efficiently outlines cellular boundaries, indexes them, and calculates key cellular parameters with high accuracy. This framework will enable efficient and automated quantitative analysis of high-resolution fluorescence microscopy images to advance research into microbial adaptations to grow and metabolism that allow extremophiles to thrive in their harsh habitats.

Histo-Miner: Deep Learning based Tissue Features Extraction Pipeline from H&E Whole Slide Images of Cutaneous Squamous Cell Carcinoma

Recent advancements in digital pathology have enabled comprehensive analysis of Whole-Slide Images (WSI) from tissue samples, leveraging high-resolution microscopy and computational capabilities. Despite this progress, there is a lack of labeled datasets and open source pipelines specifically tailored for analysis of skin tissue. Here we propose Histo-Miner, a deep learning-based pipeline for analysis of skin WSIs and generate two datasets with labeled nuclei and tumor regions. We develop our pipeline for the analysis of patient samples of cutaneous squamous cell carcinoma (cSCC), a frequent non-melanoma skin cancer. Utilizing the two datasets, comprising 47,392 annotated cell nuclei and 144 tumor-segmented WSIs respectively, both from cSCC patients, Histo-Miner employs convolutional neural networks and vision transformers for nucleus segmentation and classification as well as tumor region segmentation. Performance of trained models positively compares to state of the art with multi-class Panoptic Quality (mPQ) of 0.569 for nucleus segmentation, macro-averaged F1 of 0.832 for nucleus classification and mean Intersection over Union (mIoU) of 0.884 for tumor region segmentation. From these predictions we generate a compact feature vector summarizing tissue morphology and cellular interactions, which can be used for various downstream tasks. Here, we use Histo-Miner to predict cSCC patient response to immunotherapy based on pre-treatment WSIs from 45 patients. Histo-Miner identifies percentages of lymphocytes, the granulocyte to lymphocyte ratio in tumor vicinity and the distances between granulocytes and plasma cells in tumors as predictive features for therapy response. This highlights the applicability of Histo-Miner to clinically relevant scenarios, providing direct interpretation of the classification and insights into the underlying biology.

AI-Driven High-Resolution Cell Segmentation and Quantitative Analysis

Studying the growth and metabolism of microbes provides critical insights into their evolutionary adaptations to harsh environments, which are essential for microbial research and biotechnology applications. In this study, we developed an AI-driven image analysis system to efficiently segment individual cells and quantitatively analyze key cellular features. This system is comprised of four main modules. First, a denoising algorithm enhances contrast and suppresses noise while preserving fine cellular details. Second, the Segment Anything Model (SAM) enables accurate, zero-shot segmentation of cells without additional training. Third, post-processing is applied to refine segmentation results by removing over-segmented masks. Finally, quantitative analysis algorithms extract essential cellular features, including average intensity, length, width, and volume. The results show that denoising and post-processing significantly improved the segmentation accuracy of SAM in this new domain. Without human annotations, the AI-driven pipeline automatically and efficiently outlines cellular boundaries, indexes them, and calculates key cellular parameters with high accuracy. This framework will enable efficient and automated quantitative analysis of high-resolution fluorescence microscopy images to advance research into microbial adaptations to grow and metabolism that allow extremophiles to thrive in their harsh habitats.

OG-HFYOLO :Orientation gradient guidance and heterogeneous feature fusion for deformation table cell instance segmentation

Table structure recognition is a key task in document analysis. However, the geometric deformation in deformed tables causes a weak correlation between content information and structure, resulting in downstream tasks not being able to obtain accurate content information. To obtain fine-grained spatial coordinates of cells, we propose the OG-HFYOLO model, which enhances the edge response by Gradient Orientation-aware Extractor, combines a Heterogeneous Kernel Cross Fusion module and a scale-aware loss function to adapt to multi-scale objective features, and introduces mask-driven non-maximal suppression in the post-processing, which replaces the traditional bounding box suppression mechanism. Furthermore, we also propose a data generator, filling the gap in the dataset for fine-grained deformation table cell spatial coordinate localization, and derive a large-scale dataset named Deformation Wired Table (DWTAL). Experiments show that our proposed model demonstrates excellent segmentation accuracy on all mainstream instance segmentation models. The dataset and the source code are open source: https://github.com/justliulong/OGHFYOLO.