arXiv subjects

Mehrdad Rakaee

Publications and source records attributed to Mehrdad Rakaee.

3 recordsLinked to original sources

arXiv2026

CellPrior-Net: Prior-Guided Nuclei Detection and Classification for H&E Whole-Slide Images

Accurate nuclei detection and classification in hematoxylin and eosin (H and E) whole-slide images (WSIs) is a key task in computational pathology, particularly for quantitative analysis of the tumor microenvironment. However, this task remains highly challenging due to variations in nuclei morphology, staining procedures, scanners, organs, magnifications, and WSI artifacts. In addition, many existing pipelines rely on computationally demanding architectures and post-processing procedures, making gigapixel WSI analysis time consuming. In this work, CellPriorNet (CP Net) is proposed, an efficient nuclei detection and classification pipeline that utilizes a lightweight convolutional neural network architecture and hematoxylin (H) channel as prior information to enhance nuclei-aware feature learning. Extensive benchmarking was conducted against state of the art pipelines on 8 public and private datasets (total:10.4M nuclei) obtained from different organs, scanners, magnifications, and clinical centers. Experimental results demonstrate that CP Net achieves comparable performance while significantly reducing inference time. Furthermore, CellQuant Net was introduced, an end to end nuclei quantification pipeline, that integrates a quality assessment (QA) model to exclude regions with artifacts, followed by CP-Net cell detection and classification. The pipeline is publicly available on GitHub, and provides a potentially efficient and scalable framework for downstream computational pathology applications.

cs.MM↗

arXiv2024

Fully Automatic Content-Aware Tiling Pipeline for Pathology Whole Slide Images

In recent years, the use of deep learning (DL) methods, including convolutional neural networks (CNNs) and vision transformers (ViTs), has significantly advanced computational pathology, enhancing both diagnostic accuracy and efficiency. Hematoxylin and Eosin (H&E) Whole Slide Images (WSI) plays a crucial role by providing detailed tissue samples for the analysis and training of DL models. However, WSIs often contain regions with artifacts such as tissue folds, blurring, as well as non-tissue regions (background), which can negatively impact DL model performance. These artifacts are diagnostically irrelevant and can lead to inaccurate results. This paper proposes a fully automatic supervised DL pipeline for WSI Quality Assessment (WSI-QA) that uses a fused model combining CNNs and ViTs to detect and exclude WSI regions with artifacts, ensuring that only qualified WSI regions are used to build DL-based computational pathology applications. The proposed pipeline employs a pixel-based segmentation model to classify WSI regions as either qualified or non-qualified based on the presence of artifacts. The proposed model was trained on a large and diverse dataset and validated with internal and external data from various human organs, scanners, and H&E staining procedures. Quantitative and qualitative evaluations demonstrate the superiority of the proposed model, which outperforms state-of-the-art methods in WSI artifact detection. The proposed model consistently achieved over 95% accuracy, precision, recall, and F1 score across all artifact types. Furthermore, the WSI-QA pipeline shows strong generalization across different tissue types and scanning conditions.

cs.MM↗

arXiv2024

Deep learning-based classification of breast cancer molecular subtypes from H&E whole-slide images

Classifying breast cancer molecular subtypes is crucial for tailoring treatment strategies. While immunohistochemistry (IHC) and gene expression profiling are standard methods for molecular subtyping, IHC can be subjective, and gene profiling is costly and not widely accessible in many regions. Previous approaches have highlighted the potential application of deep learning models on H&E-stained whole slide images (WSI) for molecular subtyping, but these efforts vary in their methods, datasets, and reported performance. In this work, we investigated whether H&E-stained WSIs could be solely leveraged to predict breast cancer molecular subtypes (luminal A, B, HER2-enriched, and Basal). We used 1,433 WSIs of breast cancer in a two-step pipeline: first, classifying tumor and non-tumor tiles to use only the tumor regions for molecular subtyping; and second, employing a One-vs-Rest (OvR) strategy to train four binary OvR classifiers and aggregating their results using an eXtreme Gradient Boosting (XGBoost) model. The pipeline was tested on 221 hold-out WSIs, achieving an overall macro F1 score of 0.95 for tumor detection and 0.73 for molecular subtyping. Our findings suggest that, with further validation, supervised deep learning models could serve as supportive tools for molecular subtyping in breast cancer. Our codes are made available to facilitate ongoing research and development.

eess.IV↗