arXiv subjects

Josien P. W. Pluim

Publications and source records attributed to Josien P. W. Pluim.

45 records · Page 3Linked to original sources

arXiv2018

Not-so-supervised: a survey of semi-supervised, multi-instance, and transfer learning in medical image analysis

Machine learning (ML) algorithms have made a tremendous impact in the field of medical imaging. While medical imaging datasets have been growing in size, a challenge for supervised ML algorithms that is frequently mentioned is the lack of annotated data. As a result, various methods which can learn with less/other types of supervision, have been proposed. We review semi-supervised, multiple instance, and transfer learning in medical imaging, both in diagnosis/detection or segmentation tasks. We also discuss connections between these learning scenarios, and opportunities for future research.

cs.CV↗

arXiv2018

Crowd disagreement about medical images is informative

Classifiers for medical image analysis are often trained with a single consensus label, based on combining labels given by experts or crowds. However, disagreement between annotators may be informative, and thus removing it may not be the best strategy. As a proof of concept, we predict whether a skin lesion from the ISIC 2017 dataset is a melanoma or not, based on crowd annotations of visual characteristics of that lesion. We compare using the mean annotations, illustrating consensus, to standard deviations and other distribution moments, illustrating disagreement. We show that the mean annotations perform best, but that the disagreement measures are still informative. We also make the crowd annotations used in this paper available at \url{https://figshare.com/s/5cbbce14647b66286544}.

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arXiv2018

Inferring a Third Spatial Dimension from 2D Histological Images

Histological images are obtained by transmitting light through a tissue specimen that has been stained in order to produce contrast. This process results in 2D images of the specimen that has a three-dimensional structure. In this paper, we propose a method to infer how the stains are distributed in the direction perpendicular to the surface of the slide for a given 2D image in order to obtain a 3D representation of the tissue. This inference is achieved by decomposition of the staining concentration maps under constraints that ensure realistic decomposition and reconstruction of the original 2D images. Our study shows that it is possible to generate realistic 3D images making this method a potential tool for data augmentation when training deep learning models.

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arXiv2017

Isointense infant brain MRI segmentation with a dilated convolutional neural network

Quantitative analysis of brain MRI at the age of 6 months is difficult because of the limited contrast between white matter and gray matter. In this study, we use a dilated triplanar convolutional neural network in combination with a non-dilated 3D convolutional neural network for the segmentation of white matter, gray matter and cerebrospinal fluid in infant brain MR images, as provided by the MICCAI grand challenge on 6-month infant brain MRI segmentation.

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arXiv2017

Domain-adversarial neural networks to address the appearance variability of histopathology images

Preparing and scanning histopathology slides consists of several steps, each with a multitude of parameters. The parameters can vary between pathology labs and within the same lab over time, resulting in significant variability of the tissue appearance that hampers the generalization of automatic image analysis methods. Typically, this is addressed with ad-hoc approaches such as staining normalization that aim to reduce the appearance variability. In this paper, we propose a systematic solution based on domain-adversarial neural networks. We hypothesize that removing the domain information from the model representation leads to better generalization. We tested our hypothesis for the problem of mitosis detection in breast cancer histopathology images and made a comparative analysis with two other approaches. We show that combining color augmentation with domain-adversarial training is a better alternative than standard approaches to improve the generalization of deep learning methods.

cs.CV↗

arXiv2017

Adversarial training and dilated convolutions for brain MRI segmentation

Convolutional neural networks (CNNs) have been applied to various automatic image segmentation tasks in medical image analysis, including brain MRI segmentation. Generative adversarial networks have recently gained popularity because of their power in generating images that are difficult to distinguish from real images. In this study we use an adversarial training approach to improve CNN-based brain MRI segmentation. To this end, we include an additional loss function that motivates the network to generate segmentations that are difficult to distinguish from manual segmentations. During training, this loss function is optimised together with the conventional average per-voxel cross entropy loss. The results show improved segmentation performance using this adversarial training procedure for segmentation of two different sets of images and using two different network architectures, both visually and in terms of Dice coefficients.

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arXiv2016

Gland Segmentation in Colon Histology Images: The GlaS Challenge Contest

Colorectal adenocarcinoma originating in intestinal glandular structures is the most common form of colon cancer. In clinical practice, the morphology of intestinal glands, including architectural appearance and glandular formation, is used by pathologists to inform prognosis and plan the treatment of individual patients. However, achieving good inter-observer as well as intra-observer reproducibility of cancer grading is still a major challenge in modern pathology. An automated approach which quantifies the morphology of glands is a solution to the problem. This paper provides an overview to the Gland Segmentation in Colon Histology Images Challenge Contest (GlaS) held at MICCAI'2015. Details of the challenge, including organization, dataset and evaluation criteria, are presented, along with the method descriptions and evaluation results from the top performing methods.

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arXiv2016

Cutting out the middleman: measuring nuclear area in histopathology slides without segmentation

The size of nuclei in histological preparations from excised breast tumors is predictive of patient outcome (large nuclei indicate poor outcome). Pathologists take into account nuclear size when performing breast cancer grading. In addition, the mean nuclear area (MNA) has been shown to have independent prognostic value. The straightforward approach to measuring nuclear size is by performing nuclei segmentation. We hypothesize that given an image of a tumor region with known nuclei locations, the area of the individual nuclei and region statistics such as the MNA can be reliably computed directly from the image data by employing a machine learning model, without the intermediate step of nuclei segmentation. Towards this goal, we train a deep convolutional neural network model that is applied locally at each nucleus location, and can reliably measure the area of the individual nuclei and the MNA. Furthermore, we show how such an approach can be extended to perform combined nuclei detection and measurement, which is reminiscent of granulometry.

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arXiv2014

Assessment of algorithms for mitosis detection in breast cancer histopathology images

The proliferative activity of breast tumors, which is routinely estimated by counting of mitotic figures in hematoxylin and eosin stained histology sections, is considered to be one of the most important prognostic markers. However, mitosis counting is laborious, subjective and may suffer from low inter-observer agreement. With the wider acceptance of whole slide images in pathology labs, automatic image analysis has been proposed as a potential solution for these issues. In this paper, the results from the Assessment of Mitosis Detection Algorithms 2013 (AMIDA13) challenge are described. The challenge was based on a data set consisting of 12 training and 11 testing subjects, with more than one thousand annotated mitotic figures by multiple observers. Short descriptions and results from the evaluation of eleven methods are presented. The top performing method has an error rate that is comparable to the inter-observer agreement among pathologists.

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