2,705 research outputs found
NiftyNet: a deep-learning platform for medical imaging
Medical image analysis and computer-assisted intervention problems are
increasingly being addressed with deep-learning-based solutions. Established
deep-learning platforms are flexible but do not provide specific functionality
for medical image analysis and adapting them for this application requires
substantial implementation effort. Thus, there has been substantial duplication
of effort and incompatible infrastructure developed across many research
groups. This work presents the open-source NiftyNet platform for deep learning
in medical imaging. The ambition of NiftyNet is to accelerate and simplify the
development of these solutions, and to provide a common mechanism for
disseminating research outputs for the community to use, adapt and build upon.
NiftyNet provides a modular deep-learning pipeline for a range of medical
imaging applications including segmentation, regression, image generation and
representation learning applications. Components of the NiftyNet pipeline
including data loading, data augmentation, network architectures, loss
functions and evaluation metrics are tailored to, and take advantage of, the
idiosyncracies of medical image analysis and computer-assisted intervention.
NiftyNet is built on TensorFlow and supports TensorBoard visualization of 2D
and 3D images and computational graphs by default.
We present 3 illustrative medical image analysis applications built using
NiftyNet: (1) segmentation of multiple abdominal organs from computed
tomography; (2) image regression to predict computed tomography attenuation
maps from brain magnetic resonance images; and (3) generation of simulated
ultrasound images for specified anatomical poses.
NiftyNet enables researchers to rapidly develop and distribute deep learning
solutions for segmentation, regression, image generation and representation
learning applications, or extend the platform to new applications.Comment: Wenqi Li and Eli Gibson contributed equally to this work. M. Jorge
Cardoso and Tom Vercauteren contributed equally to this work. 26 pages, 6
figures; Update includes additional applications, updated author list and
formatting for journal submissio
Explainable artificial intelligence (XAI) in deep learning-based medical image analysis
With an increase in deep learning-based methods, the call for explainability
of such methods grows, especially in high-stakes decision making areas such as
medical image analysis. This survey presents an overview of eXplainable
Artificial Intelligence (XAI) used in deep learning-based medical image
analysis. A framework of XAI criteria is introduced to classify deep
learning-based medical image analysis methods. Papers on XAI techniques in
medical image analysis are then surveyed and categorized according to the
framework and according to anatomical location. The paper concludes with an
outlook of future opportunities for XAI in medical image analysis.Comment: Submitted for publication. Comments welcome by email to first autho
Recursive Training of 2D-3D Convolutional Networks for Neuronal Boundary Detection
Efforts to automate the reconstruction of neural circuits from 3D electron
microscopic (EM) brain images are critical for the field of connectomics. An
important computation for reconstruction is the detection of neuronal
boundaries. Images acquired by serial section EM, a leading 3D EM technique,
are highly anisotropic, with inferior quality along the third dimension. For
such images, the 2D max-pooling convolutional network has set the standard for
performance at boundary detection. Here we achieve a substantial gain in
accuracy through three innovations. Following the trend towards deeper networks
for object recognition, we use a much deeper network than previously employed
for boundary detection. Second, we incorporate 3D as well as 2D filters, to
enable computations that use 3D context. Finally, we adopt a recursively
trained architecture in which a first network generates a preliminary boundary
map that is provided as input along with the original image to a second network
that generates a final boundary map. Backpropagation training is accelerated by
ZNN, a new implementation of 3D convolutional networks that uses multicore CPU
parallelism for speed. Our hybrid 2D-3D architecture could be more generally
applicable to other types of anisotropic 3D images, including video, and our
recursive framework for any image labeling problem
- …