Attention GhostUNet++: Enhanced Segmentation of Adipose Tissue and Liver in CT Images

Accurate segmentation of abdominal adipose tissue, including subcutaneous (SAT) and visceral adipose tissue (VAT), along with liver segmentation, is essential for understanding body composition and associated health risks such as type 2 diabetes and cardiovascular disease. This study proposes Attention GhostUNet++, a novel deep learning model incorporating Channel, Spatial, and Depth Attention mechanisms into the Ghost UNet++ bottleneck for automated, precise segmentation. Evaluated on the AATTCT-IDS and LiTS datasets, the model achieved Dice coefficients of 0.9430 for VAT, 0.9639 for SAT, and 0.9652 for liver segmentation, surpassing baseline models. Despite minor limitations in boundary detail segmentation, the proposed model significantly enhances feature refinement, contextual understanding, and computational efficiency, offering a robust solution for body composition analysis. The implementation of the proposed Attention GhostUNet++ model is available at:https://github.com/MansoorHayat777/Attention-GhostUNetPlusPlus.

Benchmarking Multi-Organ Segmentation Tools for Multi-Parametric T1-weighted Abdominal MRI

The segmentation of multiple organs in multi-parametric MRI studies is critical for many applications in radiology, such as correlating imaging biomarkers with disease status (e.g., cirrhosis, diabetes). Recently, three publicly available tools, such as MRSegmentator (MRSeg), TotalSegmentator MRI (TS), and TotalVibeSegmentator (VIBE), have been proposed for multi-organ segmentation in MRI. However, the performance of these tools on specific MRI sequence types has not yet been quantified. In this work, a subset of 40 volumes from the public Duke Liver Dataset was curated. The curated dataset contained 10 volumes each from the pre-contrast fat saturated T1, arterial T1w, venous T1w, and delayed T1w phases, respectively. Ten abdominal structures were manually annotated in these volumes. Next, the performance of the three public tools was benchmarked on this curated dataset. The results indicated that MRSeg obtained a Dice score of 80.7 $\pm$ 18.6 and Hausdorff Distance (HD) error of 8.9 $\pm$ 10.4 mm. It fared the best ($p < .05$) across the different sequence types in contrast to TS and VIBE.

MedSAM2: Segment Anything in 3D Medical Images and Videos

Medical image and video segmentation is a critical task for precision medicine, which has witnessed considerable progress in developing task or modality-specific and generalist models for 2D images. However, there have been limited studies on building general-purpose models for 3D images and videos with comprehensive user studies. Here, we present MedSAM2, a promptable segmentation foundation model for 3D image and video segmentation. The model is developed by fine-tuning the Segment Anything Model 2 on a large medical dataset with over 455,000 3D image-mask pairs and 76,000 frames, outperforming previous models across a wide range of organs, lesions, and imaging modalities. Furthermore, we implement a human-in-the-loop pipeline to facilitate the creation of large-scale datasets resulting in, to the best of our knowledge, the most extensive user study to date, involving the annotation of 5,000 CT lesions, 3,984 liver MRI lesions, and 251,550 echocardiogram video frames, demonstrating that MedSAM2 can reduce manual costs by more than 85%. MedSAM2 is also integrated into widely used platforms with user-friendly interfaces for local and cloud deployment, making it a practical tool for supporting efficient, scalable, and high-quality segmentation in both research and healthcare environments.

MO-CTranS: A unified multi-organ segmentation model learning from multiple heterogeneously labelled datasets

Multi-organ segmentation holds paramount significance in many clinical tasks. In practice, compared to large fully annotated datasets, multiple small datasets are often more accessible and organs are not labelled consistently. Normally, an individual model is trained for each of these datasets, which is not an effective way of using data for model learning. It remains challenging to train a single model that can robustly learn from several partially labelled datasets due to label conflict and data imbalance problems. We propose MO-CTranS: a single model that can overcome such problems. MO-CTranS contains a CNN-based encoder and a Transformer-based decoder, which are connected in a multi-resolution manner. Task-specific tokens are introduced in the decoder to help differentiate label discrepancies. Our method was evaluated and compared to several baseline models and state-of-the-art (SOTA) solutions on abdominal MRI datasets that were acquired in different views (i.e. axial and coronal) and annotated for different organs (i.e. liver, kidney, spleen). Our method achieved better performance (most were statistically significant) than the compared methods. Github link: https://github.com/naisops/MO-CTranS.

A weakly-supervised deep learning model for fast localisation and delineation of the skeleton, internal organs, and spinal canal on Whole-Body Diffusion-Weighted MRI (WB-DWI)

Background: Apparent Diffusion Coefficient (ADC) values and Total Diffusion Volume (TDV) from Whole-body diffusion-weighted MRI (WB-DWI) are recognized cancer imaging biomarkers. However, manual disease delineation for ADC and TDV measurements is unfeasible in clinical practice, demanding automation. As a first step, we propose an algorithm to generate fast and reproducible probability maps of the skeleton, adjacent internal organs (liver, spleen, urinary bladder, and kidneys), and spinal canal. Methods: We developed an automated deep-learning pipeline based on a 3D patch-based Residual U-Net architecture that localizes and delineates these anatomical structures on WB-DWI. The algorithm was trained using "soft-labels" (non-binary segmentations) derived from a computationally intensive atlas-based approach. For training and validation, we employed a multi-center WB-DWI dataset comprising 532 scans from patients with Advanced Prostate Cancer (APC) or Multiple Myeloma (MM), with testing on 45 patients. Results: Our weakly-supervised deep learning model achieved an average dice score/precision/recall of 0.66/0.6/0.73 for skeletal delineations, 0.8/0.79/0.81 for internal organs, and 0.85/0.79/0.94 for spinal canal, with surface distances consistently below 3 mm. Relative median ADC and log-transformed volume differences between automated and manual expert-defined full-body delineations were below 10% and 4%, respectively. The computational time for generating probability maps was 12x faster than the atlas-based registration algorithm (25 s vs. 5 min). An experienced radiologist rated the model's accuracy "good" or "excellent" on test datasets. Conclusion: Our model offers fast and reproducible probability maps for localizing and delineating body regions on WB-DWI, enabling ADC and TDV quantification, potentially supporting clinicians in disease staging and treatment response assessment.

Top-K Maximum Intensity Projection Priors for 3D Liver Vessel Segmentation

Liver-vessel segmentation is an essential task in the pre-operative planning of liver resection. State-of-the-art 2D or 3D convolution-based methods focusing on liver vessel segmentation on 2D CT cross-sectional views, which do not take into account the global liver-vessel topology. To maintain this global vessel topology, we rely on the underlying physics used in the CT reconstruction process, and apply this to liver-vessel segmentation. Concretely, we introduce the concept of top-k maximum intensity projections, which mimics the CT reconstruction by replacing the integral along each projection direction, with keeping the top-k maxima along each projection direction. We use these top-k maximum projections to condition a diffusion model and generate 3D liver-vessel trees. We evaluate our 3D liver-vessel segmentation on the 3D-ircadb-01 dataset, and achieve the highest Dice coefficient, intersection-over-union (IoU), and Sensitivity scores compared to prior work.

MSWAL: 3D Multi-class Segmentation of Whole Abdominal Lesions Dataset

With the significantly increasing incidence and prevalence of abdominal diseases, there is a need to embrace greater use of new innovations and technology for the diagnosis and treatment of patients. Although deep-learning methods have notably been developed to assist radiologists in diagnosing abdominal diseases, existing models have the restricted ability to segment common lesions in the abdomen due to missing annotations for typical abdominal pathologies in their training datasets. To address the limitation, we introduce MSWAL, the first 3D Multi-class Segmentation of the Whole Abdominal Lesions dataset, which broadens the coverage of various common lesion types, such as gallstones, kidney stones, liver tumors, kidney tumors, pancreatic cancer, liver cysts, and kidney cysts. With CT scans collected from 694 patients (191,417 slices) of different genders across various scanning phases, MSWAL demonstrates strong robustness and generalizability. The transfer learning experiment from MSWAL to two public datasets, LiTS and KiTS, effectively demonstrates consistent improvements, with Dice Similarity Coefficient (DSC) increase of 3.00% for liver tumors and 0.89% for kidney tumors, demonstrating that the comprehensive annotations and diverse lesion types in MSWAL facilitate effective learning across different domains and data distributions. Furthermore, we propose Inception nnU-Net, a novel segmentation framework that effectively integrates an Inception module with the nnU-Net architecture to extract information from different receptive fields, achieving significant enhancement in both voxel-level DSC and region-level F1 compared to the cutting-edge public algorithms on MSWAL. Our dataset will be released after being accepted, and the code is publicly released at https://github.com/tiuxuxsh76075/MSWAL-.

Deep Learning-Based Automated Workflow for Accurate Segmentation and Measurement of Abdominal Organs in CT Scans

Background: Automated analysis of CT scans for abdominal organ measurement is crucial for improving diagnostic efficiency and reducing inter-observer variability. Manual segmentation and measurement of organs such as the kidneys, liver, spleen, and prostate are time-consuming and subject to inconsistency, underscoring the need for automated approaches. Purpose: The purpose of this study is to develop and validate an automated workflow for the segmentation and measurement of abdominal organs in CT scans using advanced deep learning models, in order to improve accuracy, reliability, and efficiency in clinical evaluations. Methods: The proposed workflow combines nnU-Net, U-Net++ for organ segmentation, followed by a 3D RCNN model for measuring organ volumes and dimensions. The models were trained and evaluated on CT datasets with metrics such as precision, recall, and Mean Squared Error (MSE) to assess performance. Segmentation quality was verified for its adaptability to variations in patient anatomy and scanner settings. Results: The developed workflow achieved high precision and recall values, exceeding 95 for all targeted organs. The Mean Squared Error (MSE) values were low, indicating a high level of consistency between predicted and ground truth measurements. The segmentation and measurement pipeline demonstrated robust performance, providing accurate delineation and quantification of the kidneys, liver, spleen, and prostate. Conclusion: The proposed approach offers an automated, efficient, and reliable solution for abdominal organ measurement in CT scans. By significantly reducing manual intervention, this workflow enhances measurement accuracy and consistency, with potential for widespread clinical implementation. Future work will focus on expanding the approach to other organs and addressing complex pathological cases.

Cross Modality Medical Image Synthesis for Improving Liver Segmentation

Deep learning-based computer-aided diagnosis (CAD) of medical images requires large datasets. However, the lack of large publicly available labeled datasets limits the development of deep learning-based CAD systems. Generative Adversarial Networks (GANs), in particular, CycleGAN, can be used to generate new cross-domain images without paired training data. However, most CycleGAN-based synthesis methods lack the potential to overcome alignment and asymmetry between the input and generated data. We propose a two-stage technique for the synthesis of abdominal MRI using cross-modality translation of abdominal CT. We show that the synthetic data can help improve the performance of the liver segmentation network. We increase the number of abdominal MRI images through cross-modality image transformation of unpaired CT images using a CycleGAN inspired deformation invariant network called EssNet. Subsequently, we combine the synthetic MRI images with the original MRI images and use them to improve the accuracy of the U-Net on a liver segmentation task. We train the U-Net on real MRI images and then on real and synthetic MRI images. Consequently, by comparing both scenarios, we achieve an improvement in the performance of U-Net. In summary, the improvement achieved in the Intersection over Union (IoU) is 1.17%. The results show potential to address the data scarcity challenge in medical imaging.

A Reverse Mamba Attention Network for Pathological Liver Segmentation

We present RMA-Mamba, a novel architecture that advances the capabilities of vision state space models through a specialized reverse mamba attention module (RMA). The key innovation lies in RMA-Mamba's ability to capture long-range dependencies while maintaining precise local feature representation through its hierarchical processing pipeline. By integrating Vision Mamba (VMamba)'s efficient sequence modeling with RMA's targeted feature refinement, our architecture achieves superior feature learning across multiple scales. This dual-mechanism approach enables robust handling of complex morphological patterns while maintaining computational efficiency. We demonstrate RMA-Mamba's effectiveness in the challenging domain of pathological liver segmentation (from both CT and MRI), where traditional segmentation approaches often fail due to tissue variations. When evaluated on a newly introduced cirrhotic liver dataset (CirrMRI600+) of T2-weighted MRI scans, RMA-Mamba achieves the state-of-the-art performance with a Dice coefficient of 92.08%, mean IoU of 87.36%, and recall of 92.96%. The architecture's generalizability is further validated on the cancerous liver segmentation from CT scans (LiTS: Liver Tumor Segmentation dataset), yielding a Dice score of 92.9% and mIoU of 88.99%. The source code of the proposed RMA-Mamba is available at https://github.com/JunZengz/RMAMamba.