Saqib Qamar

Saqib Qamar, Mohd Fazil, Parvez Ahmad et al.

Medical image segmentation plays an important role in various clinical applications; however, existing deep learning models face trade-offs between efficiency and accuracy. Convolutional Neural Networks (CNNs) capture local details well but miss the global context, whereas transformers handle the global context but at a high computational cost. Recently, State Space Sequence Models (SSMs) have shown potential for capturing long-range dependencies with linear complexity; however, their direct use in medical image segmentation remains limited due to incompatibility with image structures and autoregressive assumptions. To overcome these challenges, we propose SAMA-UNet, a novel U-shaped architecture that introduces two key innovations. First, the Self-Adaptive Mamba-like Aggregated Attention (SAMA) block adaptively integrates local and global features through dynamic attention weighting, enabling an efficient representation of complex anatomical patterns. Second, the causal resonance multi-scale module (CR-MSM) improves encoder-decoder interactions by adjusting feature resolution and causal dependencies across scales, enhancing the semantic alignment between low- and high-level features. Extensive experiments on MRI, CT, and endoscopy datasets demonstrate that SAMA-UNet consistently outperforms CNN, Transformer, and Mamba-based methods. It achieves 85.38% DSC and 87.82% NSD on BTCV, 92.16% and 96.54% on ACDC, 67.14% and 68.70% on EndoVis17, and 84.06% and 88.47% on ATLAS23, establishing new benchmarks across modalities. These results confirm the effectiveness of SAMA-UNet in combining efficiency and accuracy, making it a promising solution for real-world clinical segmentation tasks. The source code is available on GitHub.

Saqib Qamar, Syed Furqan Qadri, Roobaea Alroobaea et al.

Melanoma is a malignant tumor that originates from skin cell lesions. Accurate and efficient segmentation of skin lesions is essential for quantitative analysis but remains a challenge due to blurred lesion boundaries, gradual color changes, and irregular shapes. To address this, we propose ScaleFusionNet, a hybrid model that integrates a Cross-Attention Transformer Module (CATM) and adaptive fusion block (AFB) to enhance feature extraction and fusion by capturing both local and global features. We introduce CATM, which utilizes Swin transformer blocks and Cross Attention Fusion (CAF) to adaptively refine feature fusion and reduce semantic gaps in the encoder-decoder to improve segmentation accuracy. Additionally, the AFB uses Swin Transformer-based attention and deformable convolution-based adaptive feature extraction to help the model gather local and global contextual information through parallel pathways. This enhancement refines the lesion boundaries and preserves fine-grained details. ScaleFusionNet achieves Dice scores of 92.94\% and 91.80\% on the ISIC-2016 and ISIC-2018 datasets, respectively, demonstrating its effectiveness in skin lesion analysis. Simultaneously, independent validation experiments were conducted on the PH$^2$ dataset using the pretrained model weights. The results show that ScaleFusionNet demonstrates significant performance improvements compared with other state-of-the-art methods. Our code implementation is publicly available at GitHub.

Saqib Qamar, Abu Imran Baba, Stéphane Verger et al.

Wood comprises different cell types, such as fibers, tracheids and vessels, defining its properties. Studying cells' shape, size, and arrangement in microscopy images is crucial for understanding wood characteristics. Typically, this involves macerating (soaking) samples in a solution to separate cells, then spreading them on slides for imaging with a microscope that covers a wide area, capturing thousands of cells. However, these cells often cluster and overlap in images, making the segmentation difficult and time-consuming using standard image-processing methods. In this work, we developed an automatic deep learning segmentation approach that utilizes the one-stage YOLOv8 model for fast and accurate segmentation and characterization of macerated fiber and vessel form aspen trees in microscopy images. The model can analyze 32,640 x 25,920 pixels images and demonstrate effective cell detection and segmentation, achieving a mAP_{0.5-0.95} of 78 %. To assess the model's robustness, we examined fibers from a genetically modified tree line known for longer fibers. The outcomes were comparable to previous manual measurements. Additionally, we created a user-friendly web application for image analysis and provided the code for use on Google Colab. By leveraging YOLOv8's advances, this work provides a deep learning solution to enable efficient quantification and analysis of wood cells suitable for practical applications.

Saqib Qamar

Automated skin lesion segmentation through dermoscopic analysis is essential for early skin cancer detection, yet remains challenging due to limited annotated training data. We present MIRA-U, a semi-supervised framework that combines uncertainty-aware teacher-student pseudo-labeling with a hybrid CNN-Transformer architecture. Our approach employs a teacher network pre-trained via masked image modeling to generate confidence-weighted soft pseudo-labels, which guide a U-shaped CNN-Transformer student network featuring cross-attention skip connections. This design enhances pseudo-label quality and boundary delineation, surpassing reconstruction-based and CNN-only baselines, particularly in low-annotation regimes. Extensive evaluation on ISIC-2016 and PH2 datasets demonstrates superior performance, achieving a Dice Similarity Coefficient (DSC) of 0.9153 and Intersection over Union (IoU) of 0.8552 using only 50% labeled data. Code is publicly available on GitHub.

Saqib Qamar, Parvez Ahmad, Linlin Shen

The brain tumor segmentation task aims to classify tissue into the whole tumor (WT), tumor core (TC), and enhancing tumor (ET) classes using multimodel MRI images. Quantitative analysis of brain tumors is critical for clinical decision making. While manual segmentation is tedious, time-consuming, and subjective, this task is at the same time very challenging to automatic segmentation methods. Thanks to the powerful learning ability, convolutional neural networks (CNNs), mainly fully convolutional networks, have shown promising brain tumor segmentation. This paper further boosts the performance of brain tumor segmentation by proposing hyperdense inception 3D UNet (HI-Net), which captures multi-scale information by stacking factorization of 3D weighted convolutional layers in the residual inception block. We use hyper dense connections among factorized convolutional layers to extract more contexual information, with the help of features reusability. We use a dice loss function to cope with class imbalances. We validate the proposed architecture on the multi-modal brain tumor segmentation challenges (BRATS) 2020 testing dataset. Preliminary results on the BRATS 2020 testing set show that achieved by our proposed approach, the dice (DSC) scores of ET, WT, and TC are 0.79457, 0.87494, and 0.83712, respectively.

Parvez Ahmad, Saqib Qamar, Linlin Shen et al.

Deep convolutional neural network (CNN) achieves remarkable performance for medical image analysis. UNet is the primary source in the performance of 3D CNN architectures for medical imaging tasks, including brain tumor segmentation. The skip connection in the UNet architecture concatenates features from both encoder and decoder paths to extract multi-contextual information from image data. The multi-scaled features play an essential role in brain tumor segmentation. However, the limited use of features can degrade the performance of the UNet approach for segmentation. In this paper, we propose a modified UNet architecture for brain tumor segmentation. In the proposed architecture, we used densely connected blocks in both encoder and decoder paths to extract multi-contextual information from the concept of feature reusability. In addition, residual-inception blocks (RIB) are used to extract the local and global information by merging features of different kernel sizes. We validate the proposed architecture on the multi-modal brain tumor segmentation challenge (BRATS) 2020 testing dataset. The dice (DSC) scores of the whole tumor (WT), tumor core (TC), and enhancing tumor (ET) are 89.12%, 84.74%, and 79.12%, respectively.