Quantizing deep neural networks ,reducing the precision (bit-width) of their computations, can remarkably decrease memory usage and accelerate processing, making these models more suitable for large-scale medical imaging applications with limited computational resources. However, many existing methods studied "fake quantization", which simulates lower precision operations during inference, but does not actually reduce model size or improve real-world inference speed. Moreover, the potential of deploying real 3D low-bit quantization on modern GPUs is still unexplored. In this study, we introduce a real post-training quantization (PTQ) framework that successfully implements true 8-bit quantization on state-of-the-art (SOTA) 3D medical segmentation models, i.e., U-Net, SegResNet, SwinUNETR, nnU-Net, UNesT, TransUNet, ST-UNet,and VISTA3D. Our approach involves two main steps. First, we use TensorRT to perform fake quantization for both weights and activations with unlabeled calibration dataset. Second, we convert this fake quantization into real quantization via TensorRT engine on real GPUs, resulting in real-world reductions in model size and inference latency. Extensive experiments demonstrate that our framework effectively performs 8-bit quantization on GPUs without sacrificing model performance. This advancement enables the deployment of efficient deep learning models in medical imaging applications where computational resources are constrained. The code and models have been released, including U-Net, TransUNet pretrained on the BTCV dataset for abdominal (13-label) segmentation, UNesT pretrained on the Whole Brain Dataset for whole brain (133-label) segmentation, and nnU-Net, SegResNet, SwinUNETR and VISTA3D pretrained on TotalSegmentator V2 for full body (104-label) segmentation. https://github.com/hrlblab/PTQ.

Interactive segmentation, an integration of AI algorithms and human expertise, premises to improve the accuracy and efficiency of curating large-scale, detailed-annotated datasets in healthcare. Human experts revise the annotations predicted by AI, and in turn, AI improves its predictions by learning from these revised annotations. This interactive process continues to enhance the quality of annotations until no major revision is needed from experts. The key challenge is how to leverage AI predicted and expert revised annotations to iteratively improve the AI. Two problems arise: (1) The risk of catastrophic forgetting--the AI tends to forget the previously learned classes if it is only retrained using the expert revised classes. (2) Computational inefficiency when retraining the AI using both AI predicted and expert revised annotations; moreover, given the dominant AI predicted annotations in the dataset, the contribution of newly revised annotations--often account for a very small fraction--to the AI training remains marginal. This paper proposes Continual Tuning to address the problems from two perspectives: network design and data reuse. Firstly, we design a shared network for all classes followed by class-specific networks dedicated to individual classes. To mitigate forgetting, we freeze the shared network for previously learned classes and only update the class-specific network for revised classes. Secondly, we reuse a small fraction of data with previous annotations to avoid over-computing. The selection of such data relies on the importance estimate of each data. The importance score is computed by combining the uncertainty and consistency of AI predictions. Our experiments demonstrate that Continual Tuning achieves a speed 16x greater than repeatedly training AI from scratch without compromising the performance.

Prior to the deep learning era, shape was commonly used to describe the objects. Nowadays, state-of-the-art (SOTA) algorithms in medical imaging are predominantly diverging from computer vision, where voxel grids, meshes, point clouds, and implicit surface models are used. This is seen from numerous shape-related publications in premier vision conferences as well as the growing popularity of ShapeNet (about 51,300 models) and Princeton ModelNet (127,915 models). For the medical domain, we present a large collection of anatomical shapes (e.g., bones, organs, vessels) and 3D models of surgical instrument, called MedShapeNet, created to facilitate the translation of data-driven vision algorithms to medical applications and to adapt SOTA vision algorithms to medical problems. As a unique feature, we directly model the majority of shapes on the imaging data of real patients. As of today, MedShapeNet includes 23 dataset with more than 100,000 shapes that are paired with annotations (ground truth). Our data is freely accessible via a web interface and a Python application programming interface (API) and can be used for discriminative, reconstructive, and variational benchmarks as well as various applications in virtual, augmented, or mixed reality, and 3D printing. Exemplary, we present use cases in the fields of classification of brain tumors, facial and skull reconstructions, multi-class anatomy completion, education, and 3D printing. In future, we will extend the data and improve the interfaces. The project pages are: https://medshapenet.ikim.nrw/ and https://github.com/Jianningli/medshapenet-feedback

Annotating medical images, particularly for organ segmentation, is laborious and time-consuming. For example, annotating an abdominal organ requires an estimated rate of 30-60 minutes per CT volume based on the expertise of an annotator and the size, visibility, and complexity of the organ. Therefore, publicly available datasets for multi-organ segmentation are often limited in data size and organ diversity. This paper proposes an active learning method to expedite the annotation process for organ segmentation and creates the largest multi-organ dataset (by far) with the spleen, liver, kidneys, stomach, gallbladder, pancreas, aorta, and IVC annotated in 8,448 CT volumes, equating to 3.2 million slices. The conventional annotation methods would take an experienced annotator up to 1,600 weeks (or roughly 30.8 years) to complete this task. In contrast, our annotation method has accomplished this task in three weeks (based on an 8-hour workday, five days a week) while maintaining a similar or even better annotation quality. This achievement is attributed to three unique properties of our method: (1) label bias reduction using multiple pre-trained segmentation models, (2) effective error detection in the model predictions, and (3) attention guidance for annotators to make corrections on the most salient errors. Furthermore, we summarize the taxonomy of common errors made by AI algorithms and annotators. This allows for continuous revision of both AI and annotations and significantly reduces the annotation costs required to create large-scale datasets for a wider variety of medical imaging tasks.