248 research outputs found
Gland Instance Segmentation by Deep Multichannel Side Supervision
Abstract. In this paper, we propose a new image instance segmentation method that segments individual glands (instances) in colon histology images. This is a task called instance segmentation that has recently become increasingly important. The problem is challenging since not only do the glands need to be segmented from the complex background, they are also required to be individually identified. Here we leverage the idea of image-to-image prediction in recent deep learning by building a framework that automatically exploits and fuses complex multichannel information, regional and boundary patterns, with side supervision (deep supervision on side responses) in gland histology images. Our proposed system, deep multichannel side supervision (DMCS), alleviates heavy feature design due to the use of convolutional neural networks guided by side supervision. Compared to methods reported in the 2015 MICCAI Gland Segmentation Challenge, we observe state-of-the-art results based on a number of evaluation metrics
MILD-Net: Minimal Information Loss Dilated Network for Gland Instance Segmentation in Colon Histology Images
The analysis of glandular morphology within colon histopathology images is an
important step in determining the grade of colon cancer. Despite the importance
of this task, manual segmentation is laborious, time-consuming and can suffer
from subjectivity among pathologists. The rise of computational pathology has
led to the development of automated methods for gland segmentation that aim to
overcome the challenges of manual segmentation. However, this task is
non-trivial due to the large variability in glandular appearance and the
difficulty in differentiating between certain glandular and non-glandular
histological structures. Furthermore, a measure of uncertainty is essential for
diagnostic decision making. To address these challenges, we propose a fully
convolutional neural network that counters the loss of information caused by
max-pooling by re-introducing the original image at multiple points within the
network. We also use atrous spatial pyramid pooling with varying dilation rates
for preserving the resolution and multi-level aggregation. To incorporate
uncertainty, we introduce random transformations during test time for an
enhanced segmentation result that simultaneously generates an uncertainty map,
highlighting areas of ambiguity. We show that this map can be used to define a
metric for disregarding predictions with high uncertainty. The proposed network
achieves state-of-the-art performance on the GlaS challenge dataset and on a
second independent colorectal adenocarcinoma dataset. In addition, we perform
gland instance segmentation on whole-slide images from two further datasets to
highlight the generalisability of our method. As an extension, we introduce
MILD-Net+ for simultaneous gland and lumen segmentation, to increase the
diagnostic power of the network.Comment: Initial version published at Medical Imaging with Deep Learning
(MIDL) 201
Suggestive Annotation: A Deep Active Learning Framework for Biomedical Image Segmentation
Image segmentation is a fundamental problem in biomedical image analysis.
Recent advances in deep learning have achieved promising results on many
biomedical image segmentation benchmarks. However, due to large variations in
biomedical images (different modalities, image settings, objects, noise, etc),
to utilize deep learning on a new application, it usually needs a new set of
training data. This can incur a great deal of annotation effort and cost,
because only biomedical experts can annotate effectively, and often there are
too many instances in images (e.g., cells) to annotate. In this paper, we aim
to address the following question: With limited effort (e.g., time) for
annotation, what instances should be annotated in order to attain the best
performance? We present a deep active learning framework that combines fully
convolutional network (FCN) and active learning to significantly reduce
annotation effort by making judicious suggestions on the most effective
annotation areas. We utilize uncertainty and similarity information provided by
FCN and formulate a generalized version of the maximum set cover problem to
determine the most representative and uncertain areas for annotation. Extensive
experiments using the 2015 MICCAI Gland Challenge dataset and a lymph node
ultrasound image segmentation dataset show that, using annotation suggestions
by our method, state-of-the-art segmentation performance can be achieved by
using only 50% of training data.Comment: Accepted at MICCAI 201
Transitioning between Convolutional and Fully Connected Layers in Neural Networks
Digital pathology has advanced substantially over the last decade however
tumor localization continues to be a challenging problem due to highly complex
patterns and textures in the underlying tissue bed. The use of convolutional
neural networks (CNNs) to analyze such complex images has been well adopted in
digital pathology. However in recent years, the architecture of CNNs have
altered with the introduction of inception modules which have shown great
promise for classification tasks. In this paper, we propose a modified
"transition" module which learns global average pooling layers from filters of
varying sizes to encourage class-specific filters at multiple spatial
resolutions. We demonstrate the performance of the transition module in AlexNet
and ZFNet, for classifying breast tumors in two independent datasets of scanned
histology sections, of which the transition module was superior.Comment: This work is to appear at the 3rd workshop on Deep Learning in
Medical Image Analysis (DLMIA), MICCAI 201
- …