UNet++: A Nested U-Net Architecture for Medical Image Segmentation

In this paper, we present UNet++, a new, more powerful architecture for medical image segmentation. Our architecture is essentially a deeply-supervised encoder-decoder network where the encoder and decoder sub-networks are connected through a series of nested, dense skip pathways. The re-designed skip pathways aim at reducing the semantic gap between the feature maps of the encoder and decoder sub-networks. We argue that the optimizer would deal with an easier learning task when the feature maps from the decoder and encoder networks are semantically similar. We have evaluated UNet++ in comparison with U-Net and wide U-Net architectures across multiple medical image segmentation tasks: nodule segmentation in the low-dose CT scans of chest, nuclei segmentation in the microscopy images, liver segmentation in abdominal CT scans, and polyp segmentation in colonoscopy videos. Our experiments demonstrate that UNet++ with deep supervision achieves an average IoU gain of 3.9 and 3.4 points over U-Net and wide U-Net, respectively.Comment: 8 pages, 3 figures, 3 tables, accepted by 4th Deep Learning in Medical Image Analysis (DLMIA) Worksho

Automated segmentation of intracranial hemorrhages from 3D CT

Intracranial hemorrhage segmentation challenge (INSTANCE 2022) offers a platform for researchers to compare their solutions to segmentation of hemorrhage stroke regions from 3D CTs. In this work, we describe our solution to INSTANCE 2022. We use a 2D segmentation network, SegResNet from MONAI, operating slice-wise without resampling. The final submission is an ensemble of 18 models. Our solution (team name NVAUTO) achieves the top place in terms of Dice metric (0.721), and overall rank 2. It is implemented with Auto3DSeg.Comment: INSTANCE22 challenge report, MICCAI2022. arXiv admin note: substantial text overlap with arXiv:2209.0954

Automated head and neck tumor segmentation from 3D PET/CT

Head and neck tumor segmentation challenge (HECKTOR) 2022 offers a platform for researchers to compare their solutions to segmentation of tumors and lymph nodes from 3D CT and PET images. In this work, we describe our solution to HECKTOR 2022 segmentation task. We re-sample all images to a common resolution, crop around head and neck region, and train SegResNet semantic segmentation network from MONAI. We use 5-fold cross validation to select best model checkpoints. The final submission is an ensemble of 15 models from 3 runs. Our solution (team name NVAUTO) achieves the 1st place on the HECKTOR22 challenge leaderboard with an aggregated dice score of 0.78802.Comment: HECKTOR22 segmentation challenge. MICCAI 2022. arXiv admin note: text overlap with arXiv:2209.0954

Pseudo Supervised Metrics: Evaluating Unsupervised Image to Image Translation Models In Unsupervised Cross-Domain Classification Frameworks

The ability to classify images accurately and efficiently is dependent on having access to large labeled datasets and testing on data from the same domain that the model is trained on. Classification becomes more challenging when dealing with new data from a different domain, where collecting a large labeled dataset and training a new classifier from scratch is time-consuming, expensive, and sometimes infeasible or impossible. Cross-domain classification frameworks were developed to handle this data domain shift problem by utilizing unsupervised image-to-image (UI2I) translation models to translate an input image from the unlabeled domain to the labeled domain. The problem with these unsupervised models lies in their unsupervised nature. For lack of annotations, it is not possible to use the traditional supervised metrics to evaluate these translation models to pick the best-saved checkpoint model. In this paper, we introduce a new method called Pseudo Supervised Metrics that was designed specifically to support cross-domain classification applications contrary to other typically used metrics such as the FID which was designed to evaluate the model in terms of the quality of the generated image from a human-eye perspective. We show that our metric not only outperforms unsupervised metrics such as the FID, but is also highly correlated with the true supervised metrics, robust, and explainable. Furthermore, we demonstrate that it can be used as a standard metric for future research in this field by applying it to a critical real-world problem (the boiling crisis problem).Comment: arXiv admin note: text overlap with arXiv:2212.0910

A Generalized Framework for Critical Heat Flux Detection Using Unsupervised Image-to-Image Translation

This work proposes a framework developed to generalize Critical Heat Flux (CHF) detection classification models using an Unsupervised Image-to-Image (UI2I) translation model. The framework enables a typical classification model that was trained and tested on boiling images from domain A to predict boiling images coming from domain B that was never seen by the classification model. This is done by using the UI2I model to transform the domain B images to look like domain A images that the classification model is familiar with. Although CNN was used as the classification model and Fixed-Point GAN (FP-GAN) was used as the UI2I model, the framework is model agnostic. Meaning, that the framework can generalize any image classification model type, making it applicable to a variety of similar applications and not limited to the boiling crisis detection problem. It also means that the more the UI2I models advance, the better the performance of the framework.Comment: This work has been submitted to the Expert Systems With Applications Journal on Sep 25, 202

Brainomaly: Unsupervised Neurologic Disease Detection Utilizing Unannotated T1-weighted Brain MR Images

Harnessing the power of deep neural networks in the medical imaging domain is challenging due to the difficulties in acquiring large annotated datasets, especially for rare diseases, which involve high costs, time, and effort for annotation. Unsupervised disease detection methods, such as anomaly detection, can significantly reduce human effort in these scenarios. While anomaly detection typically focuses on learning from images of healthy subjects only, real-world situations often present unannotated datasets with a mixture of healthy and diseased subjects. Recent studies have demonstrated that utilizing such unannotated images can improve unsupervised disease and anomaly detection. However, these methods do not utilize knowledge specific to registered neuroimages, resulting in a subpar performance in neurologic disease detection. To address this limitation, we propose Brainomaly, a GAN-based image-to-image translation method specifically designed for neurologic disease detection. Brainomaly not only offers tailored image-to-image translation suitable for neuroimages but also leverages unannotated mixed images to achieve superior neurologic disease detection. Additionally, we address the issue of model selection for inference without annotated samples by proposing a pseudo-AUC metric, further enhancing Brainomaly's detection performance. Extensive experiments and ablation studies demonstrate that Brainomaly outperforms existing state-of-the-art unsupervised disease and anomaly detection methods by significant margins in Alzheimer's disease detection using a publicly available dataset and headache detection using an institutional dataset. The code is available from https://github.com/mahfuzmohammad/Brainomaly.Comment: Accepted in WACV 202

Fetal Brain Tissue Annotation and Segmentation Challenge Results

In-utero fetal MRI is emerging as an important tool in the diagnosis and analysis of the developing human brain. Automatic segmentation of the developing fetal brain is a vital step in the quantitative analysis of prenatal neurodevelopment both in the research and clinical context. However, manual segmentation of cerebral structures is time-consuming and prone to error and inter-observer variability. Therefore, we organized the Fetal Tissue Annotation (FeTA) Challenge in 2021 in order to encourage the development of automatic segmentation algorithms on an international level. The challenge utilized FeTA Dataset, an open dataset of fetal brain MRI reconstructions segmented into seven different tissues (external cerebrospinal fluid, grey matter, white matter, ventricles, cerebellum, brainstem, deep grey matter). 20 international teams participated in this challenge, submitting a total of 21 algorithms for evaluation. In this paper, we provide a detailed analysis of the results from both a technical and clinical perspective. All participants relied on deep learning methods, mainly U-Nets, with some variability present in the network architecture, optimization, and image pre- and post-processing. The majority of teams used existing medical imaging deep learning frameworks. The main differences between the submissions were the fine tuning done during training, and the specific pre- and post-processing steps performed. The challenge results showed that almost all submissions performed similarly. Four of the top five teams used ensemble learning methods. However, one team's algorithm performed significantly superior to the other submissions, and consisted of an asymmetrical U-Net network architecture. This paper provides a first of its kind benchmark for future automatic multi-tissue segmentation algorithms for the developing human brain in utero.Comment: Results from FeTA Challenge 2021, held at MICCAI; Manuscript submitte