Importance of Aligning Training Strategy with Evaluation for Diffusion Models in 3D Multiclass Segmentation

Recently, denoising diffusion probabilistic models (DDPM) have been applied to image segmentation by generating segmentation masks conditioned on images, while the applications were mainly limited to 2D networks without exploiting potential benefits from the 3D formulation. In this work, we studied the DDPM-based segmentation model for 3D multiclass segmentation on two large multiclass data sets (prostate MR and abdominal CT). We observed that the difference between training and test methods led to inferior performance for existing DDPM methods. To mitigate the inconsistency, we proposed a recycling method which generated corrupted masks based on the model's prediction at a previous time step instead of using ground truth. The proposed method achieved statistically significantly improved performance compared to existing DDPMs, independent of a number of other techniques for reducing train-test discrepancy, including performing mask prediction, using Dice loss, and reducing the number of diffusion time steps during training. The performance of diffusion models was also competitive and visually similar to non-diffusion-based U-net, within the same compute budget. The JAX-based diffusion framework has been released at https://github.com/mathpluscode/ImgX-DiffSeg.Comment: Accepted at Deep Generative Models workshop at MICCAI 202

Strategising template-guided needle placement for MR-targeted prostate biopsy

Clinically significant prostate cancer has a better chance to be sampled during ultrasound-guided biopsy procedures, if suspected lesions found in pre-operative magnetic resonance (MR) images are used as targets. However, the diagnostic accuracy of the biopsy procedure is limited by the operator-dependent skills and experience in sampling the targets, a sequential decision making process that involves navigating an ultrasound probe and placing a series of sampling needles for potentially multiple targets. This work aims to learn a reinforcement learning (RL) policy that optimises the actions of continuous positioning of 2D ultrasound views and biopsy needles with respect to a guiding template, such that the MR targets can be sampled efficiently and sufficiently. We first formulate the task as a Markov decision process (MDP) and construct an environment that allows the targeting actions to be performed virtually for individual patients, based on their anatomy and lesions derived from MR images. A patient-specific policy can thus be optimised, before each biopsy procedure, by rewarding positive sampling in the MDP environment. Experiment results from fifty four prostate cancer patients show that the proposed RL-learned policies obtained a mean hit rate of 93% and an average cancer core length of 11 mm, which compared favourably to two alternative baseline strategies designed by humans, without hand-engineered rewards that directly maximise these clinically relevant metrics. Perhaps more interestingly, it is found that the RL agents learned strategies that were adaptive to the lesion size, where spread of the needles was prioritised for smaller lesions. Such a strategy has not been previously reported or commonly adopted in clinical practice, but led to an overall superior targeting performance when compared with intuitively designed strategies.Comment: Paper submitted and accepted to CaPTion (Cancer Prevention through early detecTion) @ MICCAI 2022 Worksho

Boundary-RL: Reinforcement Learning for Weakly-Supervised Prostate Segmentation in TRUS Images

We propose Boundary-RL, a novel weakly supervised segmentation method that utilises only patch-level labels for training. We envision the segmentation as a boundary detection problem, rather than a pixel-level classification as in previous works. This outlook on segmentation may allow for boundary delineation under challenging scenarios such as where noise artefacts may be present within the region-of-interest (ROI) boundaries, where traditional pixel-level classification-based weakly supervised methods may not be able to effectively segment the ROI. Particularly of interest, ultrasound images, where intensity values represent acoustic impedance differences between boundaries, may also benefit from the boundary delineation approach. Our method uses reinforcement learning to train a controller function to localise boundaries of ROIs using a reward derived from a pre-trained boundary-presence classifier. The classifier indicates when an object boundary is encountered within a patch, as the controller modifies the patch location in a sequential Markov decision process. The classifier itself is trained using only binary patch-level labels of object presence, which are the only labels used during training of the entire boundary delineation framework, and serves as a weak signal to inform the boundary delineation. The use of a controller function ensures that a sliding window over the entire image is not necessary. It also prevents possible false-positive or -negative cases by minimising number of patches passed to the boundary-presence classifier. We evaluate our proposed approach for a clinically relevant task of prostate gland segmentation on trans-rectal ultrasound images. We show improved performance compared to other tested weakly supervised methods, using the same labels e.g., multiple instance learning.Comment: Accepted to MICCAI Workshop MLMI 2023 (14th International Conference on Machine Learning in Medical Imaging

Deep hashing for global registration of untracked 2D laparoscopic ultrasound to CT

PURPOSE: The registration of Laparoscopic Ultrasound (LUS) to CT can enhance the safety of laparoscopic liver surgery by providing the surgeon with awareness on the relative positioning between critical vessels and a tumour. In an effort to provide a translatable solution for this poorly constrained problem, Content-based Image Retrieval (CBIR) based on vessel information has been suggested as a method for obtaining a global coarse registration without using tracking information. However, the performance of these frameworks is limited by the use of non-generalisable handcrafted vessel features. METHODS: We propose the use of a Deep Hashing (DH) network to directly convert vessel images from both LUS and CT into fixed size hash codes. During training, these codes are learnt from a patient-specific CT scan by supplying the network with triplets of vessel images which include both a registered and a mis-registered pair. Once hash codes have been learnt, they can be used to perform registration with CBIR methods. RESULTS: We test a CBIR pipeline on 11 sequences of untracked LUS distributed across 5 clinical cases. Compared to a handcrafted feature approach, our model improves the registration success rate significantly from 48% to 61%, considering a 20 mm error as the threshold for a successful coarse registration. CONCLUSIONS: We present the first DH framework for interventional multi-modal registration tasks. The presented approach is easily generalisable to other registration problems, does not require annotated data for training, and may promote the translation of these techniques

Image quality assessment for machine learning tasks using meta-reinforcement learning

In this paper, we consider image quality assessment (IQA) as a measure of how images are amenable with respect to a given downstream task, or task amenability. When the task is performed using machine learning algorithms, such as a neural-network-based task predictor for image classification or segmentation, the performance of the task predictor provides an objective estimate of task amenability. In this work, we use an IQA controller to predict the task amenability which, itself being parameterised by neural networks, can be trained simultaneously with the task predictor. We further develop a meta-reinforcement learning framework to improve the adaptability for both IQA controllers and task predictors, such that they can be fine-tuned efficiently on new datasets or meta-tasks. We demonstrate the efficacy of the proposed task-specific, adaptable IQA approach, using two clinical applications for ultrasound-guided prostate intervention and pneumonia detection on X-ray images

Image quality assessment by overlapping task-specific and task-agnostic measures: application to prostate multiparametric MR images for cancer segmentation

Image quality assessment (IQA) in medical imaging can be used to ensure that downstream clinical tasks can be reliably performed. Quantifying the impact of an image on the specific target tasks, also named as task amenability, is needed. A task-specific IQA has recently been proposed to learn an image-amenability-predicting controller simultaneously with a target task predictor. This allows for the trained IQA controller to measure the impact an image has on the target task performance, when this task is performed using the predictor, e.g. segmentation and classification neural networks in modern clinical applications. In this work, we propose an extension to this task-specific IQA approach, by adding a task-agnostic IQA based on auto-encoding as the target task. Analysing the intersection between low-quality images, deemed by both the task-specific and task-agnostic IQA, may help to differentiate the underpinning factors that caused the poor target task performance. For example, common imaging artefacts may not adversely affect the target task, which would lead to a low task-agnostic quality and a high task-specific quality, whilst individual cases considered clinically challenging, which can not be improved by better imaging equipment or protocols, is likely to result in a high task-agnostic quality but a low task-specific quality. We first describe a flexible reward shaping strategy which allows for the adjustment of weighting between task-agnostic and task-specific quality scoring. Furthermore, we evaluate the proposed algorithm using a clinically challenging target task of prostate tumour segmentation on multiparametric magnetic resonance (mpMR) images, from 850 patients. The proposed reward shaping strategy, with appropriately weighted task-specific and task-agnostic qualities, successfully identified samples that need re-acquisition due to defected imaging process.Comment: Accepted for publication at the Journal of Machine Learning for Biomedical Imaging (MELBA) https://www.melba-journal.or

Prototypical few-shot segmentation for cross-institution male pelvic structures with spatial registration

The prowess that makes few-shot learning desirable in medical image analysis is the efficient use of the support image data, which are labelled to classify or segment new classes, a task that otherwise requires substantially more training images and expert annotations. This work describes a fully 3D prototypical few-shot segmentation algorithm, such that the trained networks can be effectively adapted to clinically interesting structures that are absent in training, using only a few labelled images from a different institute. First, to compensate for the widely recognised spatial variability between institutions in episodic adaptation of novel classes, a novel spatial registration mechanism is integrated into prototypical learning, consisting of a segmentation head and an spatial alignment module. Second, to assist the training with observed imperfect alignment, support mask conditioning module is proposed to further utilise the annotation available from the support images. Extensive experiments are presented in an application of segmenting eight anatomical structures important for interventional planning, using a data set of 589 pelvic T2-weighted MR images, acquired at seven institutes. The results demonstrate the efficacy in each of the 3D formulation, the spatial registration, and the support mask conditioning, all of which made positive contributions independently or collectively. Compared with the previously proposed 2D alternatives, the few-shot segmentation performance was improved with statistical significance, regardless whether the support data come from the same or different institutes

DeepReg: a deep learning toolkit for medical image registration

DeepReg (https://github.com/DeepRegNet/DeepReg) is a community-supported open-source toolkit for research and education in medical image registration using deep learning.Comment: Accepted in The Journal of Open Source Software (JOSS