Touchstone Benchmark: Are We on the Right Way for Evaluating AI Algorithms for Medical Segmentation?

How can we test AI performance? This question seems trivial, but it isn't. Standard benchmarks often have problems such as in-distribution and small-size test sets, oversimplified metrics, unfair comparisons, and short-term outcome pressure. As a consequence, good performance on standard benchmarks does not guarantee success in real-world scenarios. To address these problems, we present Touchstone, a large-scale collaborative segmentation benchmark of 9 types of abdominal organs. This benchmark is based on 5,195 training CT scans from 76 hospitals around the world and 5,903 testing CT scans from 11 additional hospitals. This diverse test set enhances the statistical significance of benchmark results and rigorously evaluates AI algorithms across various out-of-distribution scenarios. We invited 14 inventors of 19 AI algorithms to train their algorithms, while our team, as a third party, independently evaluated these algorithms on three test sets. In addition, we also evaluated pre-existing AI frameworks--which, differing from algorithms, are more flexible and can support different algorithms--including MONAI from NVIDIA, nnU-Net from DKFZ, and numerous other open-source frameworks. We are committed to expanding this benchmark to encourage more innovation of AI algorithms for the medical domain.

MAISI: Medical AI for Synthetic Imaging

Medical imaging analysis faces challenges such as data scarcity, high annotation costs, and privacy concerns. This paper introduces the Medical AI for Synthetic Imaging (MAISI), an innovative approach using the diffusion model to generate synthetic 3D computed tomography (CT) images to address those challenges. MAISI leverages the foundation volume compression network and the latent diffusion model to produce high-resolution CT images (up to a landmark volume dimension of 512 x 512 x 768 ) with flexible volume dimensions and voxel spacing. By incorporating ControlNet, MAISI can process organ segmentation, including 127 anatomical structures, as additional conditions and enables the generation of accurately annotated synthetic images that can be used for various downstream tasks. Our experiment results show that MAISI's capabilities in generating realistic, anatomically accurate images for diverse regions and conditions reveal its promising potential to mitigate challenges using synthetic data.

Robust Real-time Segmentation of Bio-Morphological Features in Human Cherenkov Imaging during Radiotherapy via Deep Learning

Cherenkov imaging enables real-time visualization of megavoltage X-ray or electron beam delivery to the patient during Radiation Therapy (RT). Bio-morphological features, such as vasculature, seen in these images are patient-specific signatures that can be used for verification of positioning and motion management that are essential to precise RT treatment. However until now, no concerted analysis of this biological feature-based tracking was utilized because of the slow speed and accuracy of conventional image processing for feature segmentation. This study demonstrated the first deep learning framework for such an application, achieving video frame rate processing. To address the challenge of limited annotation of these features in Cherenkov images, a transfer learning strategy was applied. A fundus photography dataset including 20,529 patch retina images with ground-truth vessel annotation was used to pre-train a ResNet segmentation framework. Subsequently, a small Cherenkov dataset (1,483 images from 212 treatment fractions of 19 breast cancer patients) with known annotated vasculature masks was used to fine-tune the model for accurate segmentation prediction. This deep learning framework achieved consistent and rapid segmentation of Cherenkov-imaged bio-morphological features on another 19 patients, including subcutaneous veins, scars, and pigmented skin. Average segmentation by the model achieved Dice score of 0.85 and required less than 0.7 milliseconds processing time per instance. The model demonstrated outstanding consistency against input image variances and speed compared to conventional manual segmentation methods, laying the foundation for online segmentation in real-time monitoring in a prospective setting.

A Short Review and Evaluation of SAM2's Performance in 3D CT Image Segmentation

Since the release of Segment Anything 2 (SAM2), the medical imaging community has been actively evaluating its performance for 3D medical image segmentation. However, different studies have employed varying evaluation pipelines, resulting in conflicting outcomes that obscure a clear understanding of SAM2's capabilities and potential applications. We shortly review existing benchmarks and point out that the SAM2 paper clearly outlines a zero-shot evaluation pipeline, which simulates user clicks iteratively for up to eight iterations. We reproduced this interactive annotation simulation on 3D CT datasets and provided the results and code~\url{https://github.com/Project-MONAI/VISTA}. Our findings reveal that directly applying SAM2 on 3D medical imaging in a zero-shot manner is far from satisfactory. It is prone to generating false positives when foreground objects disappear, and annotating more slices cannot fully offset this tendency. For smaller single-connected objects like kidney and aorta, SAM2 performs reasonably well but for most organs it is still far behind state-of-the-art 3D annotation methods. More research and innovation are needed for 3D medical imaging community to use SAM2 correctly.

HoloHisto: End-to-end Gigapixel WSI Segmentation with 4K Resolution Sequential Tokenization

In digital pathology, the traditional method for deep learning-based image segmentation typically involves a two-stage process: initially segmenting high-resolution whole slide images (WSI) into smaller patches (e.g., 256x256, 512x512, 1024x1024) and subsequently reconstructing them to their original scale. This method often struggles to capture the complex details and vast scope of WSIs. In this paper, we propose the holistic histopathology (HoloHisto) segmentation method to achieve end-to-end segmentation on gigapixel WSIs, whose maximum resolution is above 80,000$\times$70,000 pixels. HoloHisto fundamentally shifts the paradigm of WSI segmentation to an end-to-end learning fashion with 1) a large (4K) resolution base patch for elevated visual information inclusion and efficient processing, and 2) a novel sequential tokenization mechanism to properly model the contextual relationships and efficiently model the rich information from the 4K input. To our best knowledge, HoloHisto presents the first holistic approach for gigapixel resolution WSI segmentation, supporting direct I/O of complete WSI and their corresponding gigapixel masks. Under the HoloHisto platform, we unveil a random 4K sampler that transcends ultra-high resolution, delivering 31 and 10 times more pixels than standard 2D and 3D patches, respectively, for advancing computational capabilities. To facilitate efficient 4K resolution dense prediction, we leverage sequential tokenization, utilizing a pre-trained image tokenizer to group image features into a discrete token grid. To assess the performance, our team curated a new kidney pathology image segmentation (KPIs) dataset with WSI-level glomeruli segmentation from whole mouse kidneys. From the results, HoloHisto-4K delivers remarkable performance gains over previous state-of-the-art models.

HATs: Hierarchical Adaptive Taxonomy Segmentation for Panoramic Pathology Image Analysis

Panoramic image segmentation in computational pathology presents a remarkable challenge due to the morphologically complex and variably scaled anatomy. For instance, the intricate organization in kidney pathology spans multiple layers, from regions like the cortex and medulla to functional units such as glomeruli, tubules, and vessels, down to various cell types. In this paper, we propose a novel Hierarchical Adaptive Taxonomy Segmentation (HATs) method, which is designed to thoroughly segment panoramic views of kidney structures by leveraging detailed anatomical insights. Our approach entails (1) the innovative HATs technique which translates spatial relationships among 15 distinct object classes into a versatile "plug-and-play" loss function that spans across regions, functional units, and cells, (2) the incorporation of anatomical hierarchies and scale considerations into a unified simple matrix representation for all panoramic entities, (3) the adoption of the latest AI foundation model (EfficientSAM) as a feature extraction tool to boost the model's adaptability, yet eliminating the need for manual prompt generation in conventional segment anything model (SAM). Experimental findings demonstrate that the HATs method offers an efficient and effective strategy for integrating clinical insights and imaging precedents into a unified segmentation model across more than 15 categories. The official implementation is publicly available at https://github.com/hrlblab/HATs.

Enhancing Single-Slice Segmentation with 3D-to-2D Unpaired Scan Distillation

2D single-slice abdominal computed tomography (CT) enables the assessment of body habitus and organ health with low radiation exposure. However, single-slice data necessitates the use of 2D networks for segmentation, but these networks often struggle to capture contextual information effectively. Consequently, even when trained on identical datasets, 3D networks typically achieve superior segmentation results. In this work, we propose a novel 3D-to-2D distillation framework, leveraging pre-trained 3D models to enhance 2D single-slice segmentation. Specifically, we extract the prediction distribution centroid from the 3D representations, to guide the 2D student by learning intra- and inter-class correlation. Unlike traditional knowledge distillation methods that require the same data input, our approach employs unpaired 3D CT scans with any contrast to guide the 2D student model. Experiments conducted on 707 subjects from the single-slice Baltimore Longitudinal Study of Aging (BLSA) dataset demonstrate that state-of-the-art 2D multi-organ segmentation methods can benefit from the 3D teacher model, achieving enhanced performance in single-slice multi-organ segmentation. Notably, our approach demonstrates considerable efficacy in low-data regimes, outperforming the model trained with all available training subjects even when utilizing only 200 training subjects. Thus, this work underscores the potential to alleviate manual annotation burdens.

VISTA3D: Versatile Imaging SegmenTation and Annotation model for 3D Computed Tomography

Segmentation foundation models have attracted great interest, however, none of them are adequate enough for the use cases in 3D computed tomography scans (CT) images. Existing works finetune on medical images with 2D foundation models trained on natural images, but interactive segmentation, especially in 2D, is too time-consuming for 3D scans and less useful for large cohort analysis. Models that can perform out-of-the-box automatic segmentation are more desirable. However, the model trained in this way lacks the ability to perform segmentation on unseen objects like novel tumors. Thus for 3D medical image analysis, an ideal segmentation solution might expect two features: accurate out-of-the-box performance covering major organ classes, and effective adaptation or zero-shot ability to novel structures. In this paper, we discuss what features a 3D CT segmentation foundation model should have, and introduce VISTA3D, Versatile Imaging SegmenTation and Annotation model. The model is trained systematically on 11454 volumes encompassing 127 types of human anatomical structures and various lesions and provides accurate out-of-the-box segmentation. The model's design also achieves state-of-the-art zero-shot interactive segmentation in 3D. The novel model design and training recipe represent a promising step toward developing a versatile medical image foundation model. Code and model weights will be released shortly. The early version of online demo can be tried on https://build.nvidia.com/nvidia/vista-3d.

mTREE: Multi-Level Text-Guided Representation End-to-End Learning for Whole Slide Image Analysis

Multi-modal learning adeptly integrates visual and textual data, but its application to histopathology image and text analysis remains challenging, particularly with large, high-resolution images like gigapixel Whole Slide Images (WSIs). Current methods typically rely on manual region labeling or multi-stage learning to assemble local representations (e.g., patch-level) into global features (e.g., slide-level). However, there is no effective way to integrate multi-scale image representations with text data in a seamless end-to-end process. In this study, we introduce Multi-Level Text-Guided Representation End-to-End Learning (mTREE). This novel text-guided approach effectively captures multi-scale WSI representations by utilizing information from accompanying textual pathology information. mTREE innovatively combines - the localization of key areas (global-to-local) and the development of a WSI-level image-text representation (local-to-global) - into a unified, end-to-end learning framework. In this model, textual information serves a dual purpose: firstly, functioning as an attention map to accurately identify key areas, and secondly, acting as a conduit for integrating textual features into the comprehensive representation of the image. Our study demonstrates the effectiveness of mTREE through quantitative analyses in two image-related tasks: classification and survival prediction, showcasing its remarkable superiority over baselines.

Universal and Extensible Language-Vision Models for Organ Segmentation and Tumor Detection from Abdominal Computed Tomography

The advancement of artificial intelligence (AI) for organ segmentation and tumor detection is propelled by the growing availability of computed tomography (CT) datasets with detailed, per-voxel annotations. However, these AI models often struggle with flexibility for partially annotated datasets and extensibility for new classes due to limitations in the one-hot encoding, architectural design, and learning scheme. To overcome these limitations, we propose a universal, extensible framework enabling a single model, termed Universal Model, to deal with multiple public datasets and adapt to new classes (e.g., organs/tumors). Firstly, we introduce a novel language-driven parameter generator that leverages language embeddings from large language models, enriching semantic encoding compared with one-hot encoding. Secondly, the conventional output layers are replaced with lightweight, class-specific heads, allowing Universal Model to simultaneously segment 25 organs and six types of tumors and ease the addition of new classes. We train our Universal Model on 3,410 CT volumes assembled from 14 publicly available datasets and then test it on 6,173 CT volumes from four external datasets. Universal Model achieves first place on six CT tasks in the Medical Segmentation Decathlon (MSD) public leaderboard and leading performance on the Beyond The Cranial Vault (BTCV) dataset. In summary, Universal Model exhibits remarkable computational efficiency (6x faster than other dataset-specific models), demonstrates strong generalization across different hospitals, transfers well to numerous downstream tasks, and more importantly, facilitates the extensibility to new classes while alleviating the catastrophic forgetting of previously learned classes. Codes, models, and datasets are available at https://github.com/ljwztc/CLIP-Driven-Universal-Model