The aggressiveness of prostate cancer, the most common cancer in men worldwide, is primarily assessed based on histopathological data using the Gleason scoring system. While artificial intelligence (AI) has shown promise in accurately predicting Gleason scores, these predictions often lack inherent explainability, potentially leading to distrust in human-machine interactions. To address this issue, we introduce a novel dataset of 1,015 tissue microarray core images, annotated by an international group of 54 pathologists. The annotations provide detailed localized pattern descriptions for Gleason grading in line with international guidelines. Utilizing this dataset, we develop an inherently explainable AI system based on a U-Net architecture that provides predictions leveraging pathologists' terminology. This approach circumvents post-hoc explainability methods while maintaining or exceeding the performance of methods trained directly for Gleason pattern segmentation (Dice score: 0.713 $\pm$ 0.003 trained on explanations vs. 0.691 $\pm$ 0.010 trained on Gleason patterns). By employing soft labels during training, we capture the intrinsic uncertainty in the data, yielding strong results in Gleason pattern segmentation even in the context of high interobserver variability. With the release of this dataset, we aim to encourage further research into segmentation in medical tasks with high levels of subjectivity and to advance the understanding of pathologists' reasoning processes.
Recent advancements in medical vision-language pre-training models have driven significant progress in zero-shot disease recognition. However, transferring image-level knowledge to pixel-level tasks, such as lesion segmentation in 3D CT scans, remains a critical challenge. Due to the complexity and variability of pathological visual characteristics, existing methods struggle to align fine-grained lesion features not encountered during training with disease-related textual representations. In this paper, we present Malenia, a novel multi-scale lesion-level mask-attribute alignment framework, specifically designed for 3D zero-shot lesion segmentation. Malenia improves the compatibility between mask representations and their associated elemental attributes, explicitly linking the visual features of unseen lesions with the extensible knowledge learned from previously seen ones. Furthermore, we design a Cross-Modal Knowledge Injection module to enhance both visual and textual features with mutually beneficial information, effectively guiding the generation of segmentation results. Comprehensive experiments across three datasets and 12 lesion categories validate the superior performance of Malenia. Codes will be publicly available.
Renal tumors, especially renal cell carcinoma (RCC), show significant heterogeneity, posing challenges for diagnosis using radiology images such as MRI, echocardiograms, and CT scans. U-Net based deep learning techniques are emerging as a promising approach for automated medical image segmentation for minimally invasive diagnosis of renal tumors. However, current techniques need further improvements in accuracy to become clinically useful to radiologists. In this study, we present an improved U-Net based model for end-to-end automated semantic segmentation of CT scan images to identify renal tumors. The model uses residual connections across convolution layers, integrates a multi-layer feature fusion (MFF) and cross-channel attention (CCA) within encoder blocks, and incorporates skip connections augmented with additional information derived using MFF and CCA. We evaluated our model on the KiTS19 dataset, which contains data from 210 patients. For kidney segmentation, our model achieves a Dice Similarity Coefficient (DSC) of 0.97 and a Jaccard index (JI) of 0.95. For renal tumor segmentation, our model achieves a DSC of 0.96 and a JI of 0.91. Based on a comparison of available DSC scores, our model outperforms the current leading models.
Small sample instance segmentation is a very challenging task, and many existing methods follow the training strategy of meta-learning which pre-train models on support set and fine-tune on query set. The pre-training phase, which is highly task related, requires a significant amount of additional training time and the selection of datasets with close proximity to ensure effectiveness. The article proposes a novel small sample instance segmentation solution from the perspective of maximizing the utilization of existing information without increasing annotation burden and training costs. The proposed method designs two modules to address the problems encountered in small sample instance segmentation. First, it helps the model fully utilize unlabeled data by learning to generate pseudo labels, increasing the number of available samples. Second, by integrating the features of text and image, more accurate classification results can be obtained. These two modules are suitable for box-free and box-dependent frameworks. In the way, the proposed method not only improves the performance of small sample instance segmentation, but also greatly reduce reliance on pre-training. We have conducted experiments in three datasets from different scenes: on land, underwater and under microscope. As evidenced by our experiments, integrated image-text corrects the confidence of classification, and pseudo labels help the model obtain preciser masks. All the results demonstrate the effectiveness and superiority of our method.
Water segmentation is critical to disaster response and water resource management. Authorities may employ high-resolution photography to monitor rivers, lakes, and reservoirs, allowing for more proactive management in agriculture, industry, and conservation. Deep learning has improved flood monitoring by allowing models like CNNs, U-Nets, and transformers to handle large volumes of satellite and aerial data. However, these models usually have significant processing requirements, limiting their usage in real-time applications. This research proposes upgrading the SegFormer model for water segmentation by data augmentation with datasets such as ADE20K and RIWA to boost generalization. We examine how inductive bias affects attention-based models and discover that SegFormer performs better on bigger datasets. To further demonstrate the function of data augmentation, Low-Rank Adaptation (LoRA) is used to lower processing complexity while preserving accuracy. We show that the suggested Habaek model outperforms current models in segmentation, with an Intersection over Union (IoU) ranging from 0.91986 to 0.94397. In terms of F1-score, recall, accuracy, and precision, Habaek performs better than rival models, indicating its potential for real-world applications. This study highlights the need to enhance structures and include datasets for effective water segmentation.
We address the problem of extending the capabilities of vision foundation models such as DINO, SAM, and CLIP, to 3D tasks. Specifically, we introduce a novel method to uplift 2D image features into Gaussian Splatting representations of 3D scenes. Unlike traditional approaches that rely on minimizing a reconstruction loss, our method employs a simpler and more efficient feature aggregation technique, augmented by a graph diffusion mechanism. Graph diffusion refines 3D features, such as coarse segmentation masks, by leveraging 3D geometry and pairwise similarities induced by DINOv2. Our approach achieves performance comparable to the state of the art on multiple downstream tasks while delivering significant speed-ups. Notably, we obtain competitive segmentation results using generic DINOv2 features, despite DINOv2 not being trained on millions of annotated segmentation masks like SAM. When applied to CLIP features, our method demonstrates strong performance in open-vocabulary object localization tasks, highlighting the versatility of our approach.
This paper describes a new spatial correspondence representation based on paired regions-of-interest (ROIs), for medical image registration. The distinct properties of the proposed ROI-based correspondence are discussed, in the context of potential benefits in clinical applications following image registration, compared with alternative correspondence-representing approaches, such as those based on sampled displacements and spatial transformation functions. These benefits include a clear connection between learning-based image registration and segmentation, which in turn motivates two cases of image registration approaches using (pre-)trained segmentation networks. Based on the segment anything model (SAM), a vision foundation model for segmentation, we develop a new registration algorithm SAMReg, which does not require any training (or training data), gradient-based fine-tuning or prompt engineering. The proposed SAMReg models are evaluated across five real-world applications, including intra-subject registration tasks with cardiac MR and lung CT, challenging inter-subject registration scenarios with prostate MR and retinal imaging, and an additional evaluation with a non-clinical example with aerial image registration. The proposed methods outperform both intensity-based iterative algorithms and DDF-predicting learning-based networks across tested metrics including Dice and target registration errors on anatomical structures, and further demonstrates competitive performance compared to weakly-supervised registration approaches that rely on fully-segmented training data. Open source code and examples are available at: https://github.com/sqhuang0103/SAMReg.git.
Monitoring of Diffuse Intrinsic Pontine Glioma (DIPG) and Diffuse Midline Glioma (DMG) brain tumors in pediatric patients is key for assessment of treatment response. Response Assessment in Pediatric Neuro-Oncology (RAPNO) guidelines recommend the volumetric measurement of these tumors using MRI. Segmentation challenges, such as the Brain Tumor Segmentation (BraTS) Challenge, promote development of automated approaches which are replicable, generalizable and accurate, to aid in these tasks. The current study presents a novel adaptation of existing nnU-Net approaches for pediatric brain tumor segmentation, submitted to the BraTS-PEDs 2024 challenge. We apply an adapted nnU-Net with hierarchical cascades to the segmentation task of the BraTS-PEDs 2024 challenge. The residual encoder variant of nnU-Net, used as our baseline model, already provides high quality segmentations. We incorporate multiple changes to the implementation of nnU-Net and devise a novel two-stage cascaded nnU-Net to segment the substructures of brain tumors from coarse to fine. Using outputs from the nnU-Net Residual Encoder (trained to segment CC, ED, ET and NET tumor labels from T1w, T1w-CE, T2w and T2-FLAIR MRI), these are passed to two additional models one classifying ET versus NET and a second classifying CC vs ED using cascade learning. We use radiological guidelines to steer which multi parametric MRI (mpMRI) to use in these cascading models. Compared to a default nnU-Net and an ensembled nnU-net as baseline approaches, our novel method provides robust segmentations for the BraTS-PEDs 2024 challenge, achieving mean Dice scores of 0.657, 0.904, 0.703, and 0.967, and HD95 of 76.2, 10.1, 111.0, and 12.3 for the ET, NET, CC and ED, respectively.
One of the fundamental problems in computer vision is image segmentation, the task of detecting distinct regions or objects in given images. Deep Neural Networks (DNN) have been shown to be very effective in segmenting challenging images, producing convincing segmentations. There is further need for probabilistic DNNs that can reflect the uncertainties from the input images and the models into the computed segmentations, in other words, new DNNs that can generate multiple plausible segmentations and their distributions depending on the input or the model uncertainties. While there are existing probabilistic segmentation models, many of them do not take into account the geometry or shape underlying the segmented regions. In this paper, we propose a probabilistic image segmentation model that can incorporate the geometry of a segmentation. Our proposed model builds on the Probabilistic U-Net of \cite{kohl2018probabilistic} to generate probabilistic segmentations, i.e.\! multiple likely segmentations for an input image. Our model also adopts the Kendall Shape Variational Auto-Encoder of \cite{vadgama2023kendall} to encode a Kendall shape space in the latent variable layers of the prior and posterior networks of the Probabilistic U-Net. Incorporating the shape space in this manner leads to a more robust segmentation with spatially coherent regions, respecting the underlying geometry in the input images.
Time-lapse microscopy imaging is a crucial technique in biomedical studies for observing cellular behavior over time, providing essential data on cell numbers, sizes, shapes, and interactions. Manual analysis of hundreds or thousands of cells is impractical, necessitating the development of automated cell segmentation approaches. Traditional image processing methods have made significant progress in this area, but the advent of deep learning methods, particularly those using U-Net-based networks, has further enhanced performance in medical and microscopy image segmentation. However, challenges remain, particularly in accurately segmenting touching cells in images with low signal-to-noise ratios. Existing methods often struggle with effectively integrating features across different levels of abstraction. This can lead to model confusion, particularly when important contextual information is lost or the features are not adequately distinguished. The challenge lies in appropriately combining these features to preserve critical details while ensuring robust and accurate segmentation. To address these issues, we propose a novel framework called RA-SE-ASPP-Net, which incorporates Residual Blocks, Attention Mechanism, Squeeze-and-Excitation connection, and Atrous Spatial Pyramid Pooling to achieve precise and robust cell segmentation. We evaluate our proposed architecture using an induced pluripotent stem cell reprogramming dataset, a challenging dataset that has received limited attention in this field. Additionally, we compare our model with different ablation experiments to demonstrate its robustness. The proposed architecture outperforms the baseline models in all evaluated metrics, providing the most accurate semantic segmentation results. Finally, we applied the watershed method to the semantic segmentation results to obtain precise segmentations with specific information for each cell.
Medical imaging is crucial for diagnosing a patient's health condition, and accurate segmentation of these images is essential for isolating regions of interest to ensure precise diagnosis and treatment planning. Existing methods primarily rely on bounding boxes or point-based prompts, while few have explored text-related prompts, despite clinicians often describing their observations and instructions in natural language. To address this gap, we first propose a RAG-based free-form text prompt generator, that leverages the domain corpus to generate diverse and realistic descriptions. Then, we introduce FLanS, a novel medical image segmentation model that handles various free-form text prompts, including professional anatomy-informed queries, anatomy-agnostic position-driven queries, and anatomy-agnostic size-driven queries. Additionally, our model also incorporates a symmetry-aware canonicalization module to ensure consistent, accurate segmentations across varying scan orientations and reduce confusion between the anatomical position of an organ and its appearance in the scan. FLanS is trained on a large-scale dataset of over 100k medical images from 7 public datasets. Comprehensive experiments demonstrate the model's superior language understanding and segmentation precision, along with a deep comprehension of the relationship between them, outperforming SOTA baselines on both in-domain and out-of-domain datasets.
Semi-supervised learning (SSL) for medical image segmentation is a challenging yet highly practical task, which reduces reliance on large-scale labeled dataset by leveraging unlabeled samples. Among SSL techniques, the weak-to-strong consistency framework, popularized by FixMatch, has emerged as a state-of-the-art method in classification tasks. Notably, such a simple pipeline has also shown competitive performance in medical image segmentation. However, two key limitations still persist, impeding its efficient adaptation: (1) the neglect of contextual dependencies results in inconsistent predictions for similar semantic features, leading to incomplete object segmentation; (2) the lack of exploitation of semantic similarity between labeled and unlabeled data induces considerable class-distribution discrepancy. To address these limitations, we propose a novel semi-supervised framework based on FixMatch, named SemSim, powered by two appealing designs from semantic similarity perspective: (1) rectifying pixel-wise prediction by reasoning about the intra-image pair-wise affinity map, thus integrating contextual dependencies explicitly into the final prediction; (2) bridging labeled and unlabeled data via a feature querying mechanism for compact class representation learning, which fully considers cross-image anatomical similarities. As the reliable semantic similarity extraction depends on robust features, we further introduce an effective spatial-aware fusion module (SFM) to explore distinctive information from multiple scales. Extensive experiments show that SemSim yields consistent improvements over the state-of-the-art methods across three public segmentation benchmarks.
Referring multi-object tracking (RMOT) is an emerging cross-modal task that aims to locate an arbitrary number of target objects and maintain their identities referred by a language expression in a video. This intricate task involves the reasoning of linguistic and visual modalities, along with the temporal association of target objects. However, the seminal work employs only loose feature fusion and overlooks the utilization of long-term information on tracked objects. In this study, we introduce a compact Transformer-based method, termed TenRMOT. We conduct feature fusion at both encoding and decoding stages to fully exploit the advantages of Transformer architecture. Specifically, we incrementally perform cross-modal fusion layer-by-layer during the encoding phase. In the decoding phase, we utilize language-guided queries to probe memory features for accurate prediction of the desired objects. Moreover, we introduce a query update module that explicitly leverages temporal prior information of the tracked objects to enhance the consistency of their trajectories. In addition, we introduce a novel task called Referring Multi-Object Tracking and Segmentation (RMOTS) and construct a new dataset named Ref-KITTI Segmentation. Our dataset consists of 18 videos with 818 expressions, and each expression averages 10.7 masks, which poses a greater challenge compared to the typical single mask in most existing referring video segmentation datasets. TenRMOT demonstrates superior performance on both the referring multi-object tracking and the segmentation tasks.
The skull segmentation from CT scans can be seen as an already solved problem. However, in MR this task has a significantly greater complexity due to the presence of soft tissues rather than bones. Capturing the bone structures from MR images of the head, where the main visualization objective is the brain, is very demanding. The attempts that make use of skull stripping seem to not be well suited for this task and fail to work in many cases. On the other hand, supervised approaches require costly and time-consuming skull annotations. To overcome the difficulties we propose a fully unsupervised approach, where we do not perform the segmentation directly on MR images, but we rather perform a synthetic CT data generation via MR-to-CT translation and perform the segmentation there. We address many issues associated with unsupervised skull segmentation including the unpaired nature of MR and CT datasets (contrastive learning), low resolution and poor quality (super-resolution), and generalization capabilities. The research has a significant value for downstream tasks requiring skull segmentation from MR volumes such as craniectomy or surgery planning and can be seen as an important step towards the utilization of synthetic data in medical imaging.
Automated vehicles rely on an accurate and robust perception of the environment. Similarly to automated cars, highly automated trains require an environmental perception. Although there is a lot of research based on either camera or LiDAR sensors in the automotive domain, very few contributions for this task exist yet for automated trains. Additionally, no public dataset or described approach for a 3D LiDAR semantic segmentation in the railway environment exists yet. Thus, we propose an approach for a point-wise 3D semantic segmentation based on the 2DPass network architecture using scans and images jointly. In addition, we present a semi-automated intelligent data annotation approach, which we use to efficiently and accurately label the required dataset recorded on a railway track in Germany. To improve performance despite a still small number of labeled scans, we apply an active learning approach to intelligently select scans for the training dataset. Our contributions are threefold: We annotate rail data including camera and LiDAR data from the railway environment, transfer label the raw LiDAR point clouds using an image segmentation network, and train a state-of-the-art 3D LiDAR semantic segmentation network efficiently leveraging active learning. The trained network achieves good segmentation results with a mean IoU of 71.48% of 9 classes.
Referring 3D Segmentation is a visual-language task that segments all points of the specified object from a 3D point cloud described by a sentence of query. Previous works perform a two-stage paradigm, first conducting language-agnostic instance segmentation then matching with given text query. However, the semantic concepts from text query and visual cues are separately interacted during the training, and both instance and semantic labels for each object are required, which is time consuming and human-labor intensive. To mitigate these issues, we propose a novel Referring 3D Segmentation pipeline, Label-Efficient and Single-Stage, dubbed LESS, which is only under the supervision of efficient binary mask. Specifically, we design a Point-Word Cross-Modal Alignment module for aligning the fine-grained features of points and textual embedding. Query Mask Predictor module and Query-Sentence Alignment module are introduced for coarse-grained alignment between masks and query. Furthermore, we propose an area regularization loss, which coarsely reduces irrelevant background predictions on a large scale. Besides, a point-to-point contrastive loss is proposed concentrating on distinguishing points with subtly similar features. Through extensive experiments, we achieve state-of-the-art performance on ScanRefer dataset by surpassing the previous methods about 3.7% mIoU using only binary labels. Code is available at https://github.com/mellody11/LESS.
Recent advancements in artificial intelligence (AI) have precipitated a paradigm shift in medical imaging, particularly revolutionizing the domain of brain imaging. This paper systematically investigates the integration of deep learning -- a principal branch of AI -- into the semantic segmentation of brain images. Semantic segmentation serves as an indispensable technique for the delineation of discrete anatomical structures and the identification of pathological markers, essential for the diagnosis of complex neurological disorders. Historically, the reliance on manual interpretation by radiologists, while noteworthy for its accuracy, is plagued by inherent subjectivity and inter-observer variability. This limitation becomes more pronounced with the exponential increase in imaging data, which traditional methods struggle to process efficiently and effectively. In response to these challenges, this study introduces the application of adversarial neural networks, a novel AI approach that not only automates but also refines the semantic segmentation process. By leveraging these advanced neural networks, our approach enhances the precision of diagnostic outputs, reducing human error and increasing the throughput of imaging data analysis. The paper provides a detailed discussion on how adversarial neural networks facilitate a more robust, objective, and scalable solution, thereby significantly improving diagnostic accuracies in neurological evaluations. This exploration highlights the transformative impact of AI on medical imaging, setting a new benchmark for future research and clinical practice in neurology.
Osteochondrodysplasia, affecting 2-3% of newborns globally, is a group of bone and cartilage disorders that often result in head malformations, contributing to childhood morbidity and reduced quality of life. Current research on this disease using mouse models faces challenges since it involves accurately segmenting the developing cartilage in 3D micro-CT images of embryonic mice. Tackling this segmentation task with deep learning (DL) methods is laborious due to the big burden of manual image annotation, expensive due to the high acquisition costs of 3D micro-CT images, and difficult due to embryonic cartilage's complex and rapidly changing shapes. While DL approaches have been proposed to automate cartilage segmentation, most such models have limited accuracy and generalizability, especially across data from different embryonic age groups. To address these limitations, we propose novel DL methods that can be adopted by any DL architectures -- including CNNs, Transformers, or hybrid models -- which effectively leverage age and spatial information to enhance model performance. Specifically, we propose two new mechanisms, one conditioned on discrete age categories and the other on continuous image crop locations, to enable an accurate representation of cartilage shape changes across ages and local shape details throughout the cranial region. Extensive experiments on multi-age cartilage segmentation datasets show significant and consistent performance improvements when integrating our conditional modules into popular DL segmentation architectures. On average, we achieve a 1.7% Dice score increase with minimal computational overhead and a 7.5% improvement on unseen data. These results highlight the potential of our approach for developing robust, universal models capable of handling diverse datasets with limited annotated data, a key challenge in DL-based medical image analysis.
This paper presents a method for generating large-scale datasets to improve class-agnostic video segmentation across robots with different form factors. Specifically, we consider the question of whether video segmentation models trained on generic segmentation data could be more effective for particular robot platforms if robot embodiment is factored into the data generation process. To answer this question, a pipeline is formulated for using 3D reconstructions (e.g. from HM3DSem) to generate segmented videos that are configurable based on a robot's embodiment (e.g. sensor type, sensor placement, and illumination source). A resulting massive RGB-D video panoptic segmentation dataset (MVPd) is introduced for extensive benchmarking with foundation and video segmentation models, as well as to support embodiment-focused research in video segmentation. Our experimental findings demonstrate that using MVPd for finetuning can lead to performance improvements when transferring foundation models to certain robot embodiments, such as specific camera placements. These experiments also show that using 3D modalities (depth images and camera pose) can lead to improvements in video segmentation accuracy and consistency. The project webpage is available at https://topipari.com/projects/MVPd
In this paper, we address the vision-based autonomous landing problem in complex urban environments using deep neural networks for semantic segmentation and risk assessment. We propose employing the SegFormer, a state-of-the-art visual transformer network, for the semantic segmentation of complex, unstructured urban environments. This approach yields valuable information that can be utilized in smart autonomous landing missions, particularly in emergency landing scenarios resulting from system failures or human errors. The assessment is done in real-time flight, when images of an RGB camera at the Unmanned Aerial Vehicle (UAV) are segmented with the SegFormer into the most common classes found in urban environments. These classes are then mapped into a level of risk, considering in general, potential material damage, damaging the drone itself and endanger people. The proposed strategy is validated through several case studies, demonstrating the huge potential of semantic segmentation-based strategies to determining the safest landing areas for autonomous emergency landing, which we believe will help unleash the full potential of UAVs on civil applications within urban areas.