arXiv subjects

Falah Jabar

Publications and source records attributed to Falah Jabar.

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

Globally and Locally Optimized Pannini Projection for High FoV Rendering of 360-degree Images

To render a spherical (360 degree or omnidirectional) image on planar displays, a 2D image -- called as viewport -- must be obtained by projecting a sphere region on a plane, according to the users viewing direction and a predefined field of view (FoV). However, any sphere to plan projection introduces geometric distortions, such as object stretching and/or bending of straight lines, which intensity increases with the considered FoV. In this paper, a fully automatic content-aware projection is proposed, aiming to reduce the geometric distortions when high FoVs are used. This new projection is based on the Pannini projection, whose parameters are firstly globally optimized according to the image content, followed by a local conformality improvement of relevant viewport objects. A crowdsourcing subjective test showed that the proposed projection is the most preferred solution among the considered state-of-the-art sphere to plan projections, producing viewports with a more pleasant visual quality.

cs.MM↗