Segmentation in large-scale cellular electron microscopy with deep learning: A literature survey

Electron microscopy (EM) enables high-resolution imaging of tissues and cells based on 2D and 3D imaging techniques. Due to the laborious and time-consuming nature of manual segmentation of large-scale EM datasets, automated segmentation approaches are crucial. This review focuses on the progress of deep learning-based segmentation techniques in large-scale cellular EM throughout the last six years, during which significant progress has been made in both semantic and instance segmentation. A detailed account is given for the key datasets that contributed to the proliferation of deep learning in 2D and 3D EM segmentation. The review covers supervised, unsupervised, and self-supervised learning methods and examines how these algorithms were adapted to the task of segmenting cellular and sub-cellular structures in EM images. The special challenges posed by such images, like heterogeneity and spatial complexity, and the network architectures that overcame some of them are described. Moreover, an overview of the evaluation measures used to benchmark EM datasets in various segmentation tasks is provided. Finally, an outlook of current trends and future prospects of EM segmentation is given, especially with large-scale models and unlabeled images to learn generic features across EM datasets

MIS-FM: 3D Medical Image Segmentation using Foundation Models Pretrained on a Large-Scale Unannotated Dataset

Pretraining with large-scale 3D volumes has a potential for improving the segmentation performance on a target medical image dataset where the training images and annotations are limited. Due to the high cost of acquiring pixel-level segmentation annotations on the large-scale pretraining dataset, pretraining with unannotated images is highly desirable. In this work, we propose a novel self-supervised learning strategy named Volume Fusion (VF) for pretraining 3D segmentation models. It fuses several random patches from a foreground sub-volume to a background sub-volume based on a predefined set of discrete fusion coefficients, and forces the model to predict the fusion coefficient of each voxel, which is formulated as a self-supervised segmentation task without manual annotations. Additionally, we propose a novel network architecture based on parallel convolution and transformer blocks that is suitable to be transferred to different downstream segmentation tasks with various scales of organs and lesions. The proposed model was pretrained with 110k unannotated 3D CT volumes, and experiments with different downstream segmentation targets including head and neck organs, thoracic/abdominal organs showed that our pretrained model largely outperformed training from scratch and several state-of-the-art self-supervised training methods and segmentation models. The code and pretrained model are available at https://github.com/openmedlab/MIS-FM.Comment: 13 pages, 8 figure

A Survey on Deep Learning in Medical Image Analysis

Deep learning algorithms, in particular convolutional networks, have rapidly become a methodology of choice for analyzing medical images. This paper reviews the major deep learning concepts pertinent to medical image analysis and summarizes over 300 contributions to the field, most of which appeared in the last year. We survey the use of deep learning for image classification, object detection, segmentation, registration, and other tasks and provide concise overviews of studies per application area. Open challenges and directions for future research are discussed.Comment: Revised survey includes expanded discussion section and reworked introductory section on common deep architectures. Added missed papers from before Feb 1st 201

Offline and Online Interactive Frameworks for MRI and CT Image Analysis in the Healthcare Domain : The Case of COVID-19, Brain Tumors and Pancreatic Tumors

Medical imaging represents the organs, tissues and structures underneath the outer layers of skin and bones etc. and stores information on normal anatomical structures for abnormality detection and diagnosis. In this thesis, tools and techniques are used to automate the analysis of medical images, emphasizing the detection of brain tumor anomalies from brain MRIs, Covid infections from lung CT images and pancreatic tumor from pancreatic CT images. Image processing methods such as filtering and thresholding models, geometry models, graph models, region-based analysis, connected component analysis, machine learning models, and recent deep learning models are used. The following problems for medical images : abnormality detection, abnormal region segmentation, interactive user interface to represent the results of detection and segmentation while receiving feedbacks from healthcare professionals to improve the analysis procedure, and finally report generation, are considered in this research. Complete interactive systems containing conventional models, machine learning, and deep learning methods for different types of medical abnormalities have been proposed and developed in this thesis. The experimental results show promising outcomes that has led to the incorporation of the methods for the proposed solutions based on the observations of the performance metrics and their comparisons. Although currently separate systems have been developed for brain tumor, Covid and pancreatic cancer, the success of the developed systems show a promising potential to combine them to form a generalized system for analyzing medical imaging of different types collected from any organs to detect any type of abnormalities

Advancing efficiency and robustness of neural networks for imaging

Enabling machines to see and analyze the world is a longstanding research objective. Advances in computer vision have the potential of influencing many aspects of our lives as they can enable machines to tackle a variety of tasks. Great progress in computer vision has been made, catalyzed by recent progress in machine learning and especially the breakthroughs achieved by deep artificial neural networks. Goal of this work is to alleviate limitations of deep neural networks that hinder their large-scale adoption for real-world applications. To this end, it investigates methodologies for constructing and training deep neural networks with low computational requirements. Moreover, it explores strategies for achieving robust performance on unseen data. Of particular interest is the application of segmenting volumetric medical scans because of the technical challenges it imposes, as well as its clinical importance. The developed methodologies are generic and of relevance to a broader computer vision and machine learning audience. More specifically, this work introduces an efficient 3D convolutional neural network architecture, which achieves high performance for segmentation of volumetric medical images, an application previously hindered by high computational requirements of 3D networks. It then investigates sensitivity of network performance on hyper-parameter configuration, which we interpret as overfitting the model configuration to the data available during development. It is shown that ensembling a set of models with diverse configurations mitigates this and improves generalization. The thesis then explores how to utilize unlabelled data for learning representations that generalize better. It investigates domain adaptation and introduces an architecture for adversarial networks tailored for adaptation of segmentation networks. Finally, a novel semi-supervised learning method is proposed that introduces a graph in the latent space of a neural network to capture relations between labelled and unlabelled samples. It then regularizes the embedding to form a compact cluster per class, which improves generalization.Open Acces

ON NEURAL ARCHITECTURES FOR SEGMENTATION IN NATURAL AND MEDICAL IMAGES

Segmentation is an important research field in computer vision. It requires recognizing and segmenting the objects at the pixel level. In the past decade, many deep neural networks have been proposed, which have been central to the development in this area. These frameworks have demonstrated human-level or beyond performance on many challenging benchmarks, and have been widely used in many real-life applications, including surveillance, autonomous driving, and medical image analysis. However, it is non-trivial to design neural architectures with both efficiency and effectiveness, especially when they need to be tailored to the target tasks and datasets. In this dissertation, I will present our research works in this area from the following aspects. (i) To enable automatic neural architecture design on the costly 3D medical image segmentation, we propose an efficient and effective neural architecture search algorithm that tackles the problem in a coarse-to-fine manner. (ii) To further take advantage of the neural architecture search, we propose to search for a channel-level replacement for 3D networks, which leads to strong alternatives to 3D networks. (iii) To perform segmentation with great detail, we design a coarse-to-fine segmentation framework for matting-level segmentation; (iv) To provide stronger features for segmentation, we propose a stronger transformer-based backbone that can work on dense tasks. (v) To better resolve the panoptic segmentation problem in an end-to-end manner, we propose to combine transformers with the traditional clustering algorithm, which leads to a more intuitive segmentation framework with better performance