Pushing the limits of cell segmentation models for imaging mass cytometry

Imaging mass cytometry (IMC) is a relatively new technique for imaging biological tissue at subcellular resolution. In recent years, learning-based segmentation methods have enabled precise quantification of cell type and morphology, but typically rely on large datasets with fully annotated ground truth (GT) labels. This paper explores the effects of imperfect labels on learning-based segmentation models and evaluates the generalisability of these models to different tissue types. Our results show that removing 50% of cell annotations from GT masks only reduces the dice similarity coefficient (DSC) score to 0.874 (from 0.889 achieved by a model trained on fully annotated GT masks). This implies that annotation time can in fact be reduced by at least half without detrimentally affecting performance. Furthermore, training our single-tissue model on imperfect labels only decreases DSC by 0.031 on an unseen tissue type compared to its multi-tissue counterpart, with negligible qualitative differences in segmentation. Additionally, bootstrapping the worst-performing model (with 5% of cell annotations) a total of ten times improves its original DSC score of 0.720 to 0.829. These findings imply that less time and work can be put into the process of producing comparable segmentation models; this includes eliminating the need for multiple IMC tissue types during training, whilst also providing the potential for models with very few labels to improve on themselves. Source code is available on GitHub: https://github.com/kimberley/ISBI2024.

Rethinking the transfer learning for FCN based polyp segmentation in colonoscopy

Besides the complex nature of colonoscopy frames with intrinsic frame formation artefacts such as light reflections and the diversity of polyp types/shapes, the publicly available polyp segmentation training datasets are limited, small and imbalanced. In this case, the automated polyp segmentation using a deep neural network remains an open challenge due to the overfitting of training on small datasets. We proposed a simple yet effective polyp segmentation pipeline that couples the segmentation (FCN) and classification (CNN) tasks. We find the effectiveness of interactive weight transfer between dense and coarse vision tasks that mitigates the overfitting in learning. And It motivates us to design a new training scheme within our segmentation pipeline. Our method is evaluated on CVC-EndoSceneStill and Kvasir-SEG datasets. It achieves 4.34% and 5.70% Polyp-IoU improvements compared to the state-of-the-art methods on the EndoSceneStill and Kvasir-SEG datasets, respectively.

Dual-stream spatiotemporal networks with feature sharing for monitoring animals in the home cage

This paper presents a spatiotemporal deep learning approach for mouse behavioural classification in the home cage. Using a series of dual-stream architectures with assorted modifications to increase performance, we introduce a novel feature-sharing approach that jointly processes the streams at regular intervals throughout the network. Using a publicly available labelled dataset of singly-housed mice, we achieve a prediction accuracy of 86.47% using an ensemble of Inception-based networks that utilize feature sharing. We also demonstrate through ablation studies that for all models, the feature-sharing architectures consistently perform better than conventional ones having separate streams. The best performing models were further evaluated on other activity datasets, both mouse and human, and achieved state-of-the-art results. Future work will investigate the effectiveness of feature sharing in behavioural classification in the unsupervised anomaly detection domain.

Unsupervised detection of mouse behavioural anomalies using two-stream convolutional autoencoders

This paper explores the application of unsupervised learning to detecting anomalies in mouse video data. The two models presented in this paper are a dual-stream, 3D convolutional autoencoder (with residual connections) and a dual-stream, 2D convolutional autoencoder. The publicly available dataset used here contains twelve videos of single home-caged mice alongside frame-level annotations. Under the pretext that the autoencoder only sees normal events, the video data was handcrafted to treat each behaviour as a pseudo-anomaly thereby eliminating them from the others during training. The results are presented for one conspicuous behaviour (hang) and one inconspicuous behaviour (groom). The performance of these models is compared to a single stream autoencoder and a supervised learning model, which are both based on the custom CAE. Both models are also tested on the CUHK Avenue dataset were found to perform as well as some state-of-the-art architectures.

DR-Unet104 for Multimodal MRI brain tumor segmentation

In this paper we propose a 2D deep residual Unet with 104 convolutional layers (DR-Unet104) for lesion segmentation in brain MRIs. We make multiple additions to the Unet architecture, including adding the 'bottleneck' residual block to the Unet encoder and adding dropout after each convolution block stack. We verified the effect of introducing the regularisation of dropout with small rate (e.g. 0.2) on the architecture, and found a dropout of 0.2 improved the overall performance compared to no dropout, or a dropout of 0.5. We evaluated the proposed architecture as part of the Multimodal Brain Tumor Segmentation (BraTS) 2020 Challenge and compared our method to DeepLabV3+ with a ResNet-V2-152 backbone. We found that the DR-Unet104 achieved a mean dice score coefficient of 0.8862, 0.6756 and 0.6721 for validation data, whole tumor, enhancing tumor and tumor core respectively, an overall improvement on 0.8770, 0.65242 and 0.68134 achieved by DeepLabV3+. Our method produced a final mean DSC of 0.8673, 0.7514 and 0.7983 on whole tumor, enhancing tumor and tumor core on the challenge's testing data. We present this as a state-of-the-art 2D lesion segmentation architecture that can be used on lower power computers than a 3D architecture. The source code and trained model for this work is openly available at https://github.com/jordan-colman/DR-Unet104.

MRI Brain Tumor Segmentation using Random Forests and Fully Convolutional Networks

In this paper, we propose a novel learning based method for automated segmentation of brain tumor in multimodal MRI images, which incorporates two sets of machine -learned and hand crafted features. Fully convolutional networks (FCN) forms the machine learned features and texton based features are considered as hand-crafted features. Random forest (RF) is used to classify the MRI image voxels into normal brain tissues and different parts of tumors, i.e. edema, necrosis and enhancing tumor. The method was evaluated on BRATS 2017 challenge dataset. The results show that the proposed method provides promising segmentations. The mean Dice overlap measure for automatic brain tumor segmentation against ground truth is 0.86, 0.78 and 0.66 for whole tumor, core and enhancing tumor, respectively.

A hybrid model for predicting human physical activity status from lifelogging data

One trend in the recent healthcare transformations is people are encouraged to monitor and manage their health based on their daily diets and physical activity habits. However, much attention of the use of operational research and analytical models in healthcare has been paid to the systematic level such as country or regional policy making or organisational issues. This paper proposes a model concerned with healthcare analytics at the individual level, which can predict human physical activity status from sequential lifelogging data collected from wearable sensors. The model has a two-stage hybrid structure (in short, MOGP-HMM) -- a multi-objective genetic programming (MOGP) algorithm in the first stage to reduce the dimensions of lifelogging data and a hidden Markov model (HMM) in the second stage for activity status prediction over time. It can be used as a decision support tool to provide real-time monitoring, statistical analysis and personalized advice to individuals, encouraging positive attitudes towards healthy lifestyles. We validate the model with the real data collected from a group of participants in the UK, and compare it with other popular two-stage hybrid models. Our experimental results show that the MOGP-HMM can achieve comparable performance. To the best of our knowledge, this is the very first study that uses the MOGP in the hybrid two-stage structure for individuals\rq{} activity status prediction. It fits seamlessly with the current trend in the UK healthcare transformation of patient empowerment as well as contributing to a strategic development for more efficient and cost-effective provision of healthcare.

Automatic individual pig detection and tracking in surveillance videos

Individual pig detection and tracking is an important requirement in many video-based pig monitoring applications. However, it still remains a challenging task in complex scenes, due to problems of light fluctuation, similar appearances of pigs, shape deformations and occlusions. To tackle these problems, we propose a robust real time multiple pig detection and tracking method which does not require manual marking or physical identification of the pigs, and works under both daylight and infrared light conditions. Our method couples a CNN-based detector and a correlation filter-based tracker via a novel hierarchical data association algorithm. The detector gains the best accuracy/speed trade-off by using the features derived from multiple layers at different scales in a one-stage prediction network. We define a tag-box for each pig as the tracking target, and the multiple object tracking is conducted in a key-points tracking manner using learned correlation filters. Under challenging conditions, the tracking failures are modelled based on the relations between responses of detector and tracker, and the data association algorithm allows the detection hypotheses to be refined, meanwhile the drifted tracks can be corrected by probing the tracking failures followed by the re-initialization of tracking. As a result, the optimal tracklets can sequentially grow with on-line refined detections, and tracking fragments are correctly integrated into respective tracks while keeping the original identifications. Experiments with a dataset captured from a commercial farm show that our method can robustly detect and track multiple pigs under challenging conditions. The promising performance of the proposed method also demonstrates a feasibility of long-term individual pig tracking in a complex environment and thus promises a commercial potential.

Fully Automatic Segmentation and Objective Assessment of Atrial Scars for Longstanding Persistent Atrial Fibrillation Patients Using Late Gadolinium-Enhanced MRI

Purpose: Atrial fibrillation (AF) is the most common cardiac arrhythmia and is correlated with increased morbidity and mortality. It is associated with atrial fibrosis, which may be assessed non-invasively using late gadolinium-enhanced (LGE) magnetic resonance imaging (MRI) where scar tissue is visualised as a region of signal enhancement. In this study, we proposed a novel fully automatic pipeline to achieve an accurate and objective atrial scarring segmentation and assessment of LGE MRI scans for the AF patients. Methods: Our fully automatic pipeline uniquely combined: (1) a multi-atlas based whole heart segmentation (MA-WHS) to determine the cardiac anatomy from an MRI Roadmap acquisition which is then mapped to LGE MRI, and (2) a super-pixel and supervised learning based approach to delineate the distribution and extent of atrial scarring in LGE MRI. Results: Both our MA-WHS and atrial scarring segmentation showed accurate delineations of cardiac anatomy (mean Dice = 89%) and atrial scarring (mean Dice =79%) respectively compared to the established ground truth from manual segmentation. Compared with previously studied methods with manual interventions, our innovative pipeline demonstrated comparable results, but was computed fully automatically. Conclusion: The proposed segmentation methods allow LGE MRI to be used as an objective assessment tool for localisation, visualisation and quantification of atrial scarring.

Deep De-Aliasing for Fast Compressive Sensing MRI

Fast Magnetic Resonance Imaging (MRI) is highly in demand for many clinical applications in order to reduce the scanning cost and improve the patient experience. This can also potentially increase the image quality by reducing the motion artefacts and contrast washout. However, once an image field of view and the desired resolution are chosen, the minimum scanning time is normally determined by the requirement of acquiring sufficient raw data to meet the Nyquist-Shannon sampling criteria. Compressive Sensing (CS) theory has been perfectly matched to the MRI scanning sequence design with much less required raw data for the image reconstruction. Inspired by recent advances in deep learning for solving various inverse problems, we propose a conditional Generative Adversarial Networks-based deep learning framework for de-aliasing and reconstructing MRI images from highly undersampled data with great promise to accelerate the data acquisition process. By coupling an innovative content loss with the adversarial loss our de-aliasing results are more realistic. Furthermore, we propose a refinement learning procedure for training the generator network, which can stabilise the training with fast convergence and less parameter tuning. We demonstrate that the proposed framework outperforms state-of-the-art CS-MRI methods, in terms of reconstruction error and perceptual image quality. In addition, our method can reconstruct each image in 0.22ms--0.37ms, which is promising for real-time applications.