Abdullah Nazib

Md Rakibul Islam, Riad Hassan, Abdullah Nazib et al.

Deep learning has achieved remarkable accuracy in medical image segmentation, particularly for larger structures with well-defined boundaries. However, its effectiveness can be challenged by factors such as irregular object shapes and edges, non-smooth surfaces, small target areas, etc. which complicate the ability of networks to grasp the intricate and diverse nature of anatomical regions. In response to these challenges, we propose an Adaptive Focal Loss (A-FL) that takes both object boundary smoothness and size into account, with the goal to improve segmentation performance in intricate anatomical regions. The proposed A-FL dynamically adjusts itself based on an object's surface smoothness, size, and the class balancing parameter based on the ratio of targeted area and background. We evaluated the performance of the A-FL on the PICAI 2022 and BraTS 2018 datasets. In the PICAI 2022 dataset, the A-FL achieved an Intersection over Union (IoU) score of 0.696 and a Dice Similarity Coefficient (DSC) of 0.769, outperforming the regular Focal Loss (FL) by 5.5% and 5.4% respectively. It also surpassed the best baseline by 2.0% and 1.2%. In the BraTS 2018 dataset, A-FL achieved an IoU score of 0.883 and a DSC score of 0.931. Our ablation experiments also show that the proposed A-FL surpasses conventional losses (this includes Dice Loss, Focal Loss, and their hybrid variants) by large margin in IoU, DSC, and other metrics. The code is available at https://github.com/rakibuliuict/AFL-CIBM.git.

Abdullah Nazib, Riad Hassan, Zahidul Islam et al.

Organ at risk (OAR) segmentation in computed tomography (CT) imagery is a difficult task for automated segmentation methods and can be crucial for downstream radiation treatment planning. U-net has become a de-facto standard for medical image segmentation and is frequently used as a common baseline in medical image segmentation tasks. In this paper, we propose a multiple decoder U-net architecture and use the segmentation disagreement between the decoders as attention to the bottleneck of the network for segmentation refinement. While feature correlation is considered as attention in most cases, in our case it is the uncertainty from the network used as attention. For accurate segmentation, we also proposed a CT intensity integrated regularization loss. Proposed regularisation helps model understand the intensity distribution of low contrast tissues. We tested our model on two publicly available OAR challenge datasets. We also conducted the ablation on each datasets with the proposed attention module and regularization loss. Experimental results demonstrate a clear accuracy improvement on both datasets.

Abdullah Nazib, Clinton Fookes, Olivier Salvado et al.

The recent application of deep learning technologies in medical image registration has exponentially decreased the registration time and gradually increased registration accuracy when compared to their traditional counterparts. Most of the learning-based registration approaches considers this task as a one directional problem. As a result, only correspondence from the moving image to the target image is considered. However, in some medical procedures bidirectional registration is required to be performed. Unlike other learning-based registration, we propose a registration framework with inverse consistency. The proposed method simultaneously learns forward transformation and backward transformation in an unsupervised manner. We perform training and testing of the method on the publicly available LPBA40 MRI dataset and demonstrate strong performance than baseline registration methods.

Abdullah Nazib, Clinton Fookes, Dimitri Perrin

The recent application of deep learning in various areas of medical image analysis has brought excellent performance gains. In particular, technologies based on deep learning in medical image registration can outperform traditional optimisation-based registration algorithms both in registration time and accuracy. However, the U-net based architectures used in most of the image registration frameworks downscale the data, which removes global information and affects the deformation. In this paper, we present a densely connected convolutional architecture for deformable image registration. Our proposed dense network downsizes data only in one stage and have dense connections instead of the skip connections in U-net architecture. The training of the network is unsupervised and does not require ground-truth deformation or any synthetic deformation as a label. The proposed architecture is trained and tested on two different versions of tissue-cleared data, at 10\% and 25\% resolution of the original single-cell-resolution dataset. We demonstrate comparable registration performance to state-of-the-art registration methods and superior performance to the deep-learning based VoxelMorph method in terms of accuracy and increased resolution handling ability. In both resolutions, the proposed DenseDeformation network outperforms VoxelMorph in registration accuracy. Importantly, it can register brains in one minute where conventional methods can take hours at 25\% resolution.

Abdullah Nazib, Clinton Fookes, Dimitri Perrin

Image registration plays an important role in comparing images. It is particularly important in analyzing medical images like CT, MRI, PET, etc. to quantify different biological samples, to monitor disease progression and to fuse different modalities to support better diagnosis. The recent emergence of tissue clearing protocols enable us to take images at cellular level resolution. Image registration tools developed for other modalities are currently unable to manage images of such extreme high resolution. The recent popularity of deep learning based methods in the computer vision community justifies a rigorous investigation of deep-learning based methods on tissue cleared images along with their traditional counterparts. In this paper, we investigate and compare the performance of a deep learning based registration method with traditional optimization based methods on samples from tissue-clearing methods. From the comparative results it is found that a deep-learning based method outperforms all traditional registration tools in terms of registration time and has achieved promising registration accuracy.

Abdullah Nazib, James Galloway, Clinton Fookes et al.

Recent progress in tissue clearing has allowed for the imaging of entire organs at single-cell resolution. These methods produce very large 3D images (several gigabytes for a whole mouse brain). A necessary step in analysing these images is registration across samples. Existing methods of registration were developed for lower resolution image modalities (e.g. MRI) and it is unclear whether their performance and accuracy is satisfactory at this larger scale. In this study, we used data from different mouse brains cleared with the CUBIC protocol to evaluate five freely available image registration tools. We used several performance metrics to assess accuracy, and completion time as a measure of efficiency. The results of this evaluation suggest that the ANTS registration tool provides the best registration accuracy while Elastix has the highest computational efficiency among the methods with an acceptable accuracy. The results also highlight the need to develop new registration methods optimised for these high-resolution 3D images.