Leigh H. Whitehead

Saúl Alonso-Monsalve, Leigh H. Whitehead, Adam Aurisano et al.

Quantitative cancer image analysis relies on the accurate delineation of tumours, a very specialised and time-consuming task. For this reason, methods for automated segmentation of tumours in medical imaging have been extensively developed in recent years, being Computed Tomography one of the most popular imaging modalities explored. However, the large amount of 3D voxels in a typical scan is prohibitive for the entire volume to be analysed at once in conventional hardware. To overcome this issue, the processes of downsampling and/or resampling are generally implemented when using traditional convolutional neural networks in medical imaging. In this paper, we propose a new methodology that introduces a process of sparsification of the input images and submanifold sparse convolutional networks as an alternative to downsampling. As a proof of concept, we applied this new methodology to Computed Tomography images of renal cancer patients, obtaining performances of segmentations of kidneys and tumours competitive with previous methods (~84.6% Dice similarity coefficient), while achieving a significant improvement in computation time (2-3 min per training epoch).

Saúl Alonso-Monsalve, Leigh H. Whitehead, Adam Aurisano et al.

The accurate delineation of tumours in radiological images like Computed Tomography is a very specialised and time-consuming task, and currently a bottleneck preventing quantitative analyses to be performed routinely in the clinical setting. For this reason, developing methods for the automated segmentation of tumours in medical imaging is of the utmost importance and has driven significant efforts in recent years. However, challenges regarding the impracticality of 3D scans, given the large amount of voxels to be analysed, usually requires the downsampling of such images or using patches thereof when applying traditional convolutional neural networks. To overcome this problem, in this paper we propose a new methodology that uses, divided into two stages, voxel sparsification and submanifold sparse convolutional networks. This method allows segmentations to be performed with high-resolution inputs and a native 3D model architecture, obtaining state-of-the-art accuracies while significantly reducing the computational resources needed in terms of GPU memory and time. We studied the deployment of this methodology in the context of Computed Tomography images of renal cancer patients from the KiTS23 challenge, and our method achieved results competitive with the challenge winners, with Dice similarity coefficients of 95.8% for kidneys + masses, 85.7% for tumours + cysts, and 80.3% for tumours alone. Crucially, our method also offers significant computational improvements, achieving up to a 60% reduction in inference time and up to a 75\% reduction in VRAM usage compared to an equivalent dense architecture, across both CPU and various GPU cards tested.

Saúl Alonso-Monsalve, Leigh H. Whitehead

We propose and demonstrate the use of a model-assisted generative adversarial network (GAN) to produce fake images that accurately match true images through the variation of the parameters of the model that describes the features of the images. The generator learns the model parameter values that produce fake images that best match the true images. Two case studies show excellent agreement between the generated best match parameters and the true parameters. The best match model parameter values can be used to retune the default simulation to minimize any bias when applying image recognition techniques to fake and true images. In the case of a real-world experiment, the true images are experimental data with unknown true model parameter values, and the fake images are produced by a simulation that takes the model parameters as input. The model-assisted GAN uses a convolutional neural network to emulate the simulation for all parameter values that, when trained, can be used as a conditional generator for fast fake-image production.