1,756 research outputs found
Automated classification of three-dimensional reconstructions of coral reefs using convolutional neural networks
© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Hopkinson, B. M., King, A. C., Owen, D. P., Johnson-Roberson, M., Long, M. H., & Bhandarkar, S. M. Automated classification of three-dimensional reconstructions of coral reefs using convolutional neural networks. PLoS One, 15(3), (2020): e0230671, doi: 10.1371/journal.pone.0230671.Coral reefs are biologically diverse and structurally complex ecosystems, which have been severally affected by human actions. Consequently, there is a need for rapid ecological assessment of coral reefs, but current approaches require time consuming manual analysis, either during a dive survey or on images collected during a survey. Reef structural complexity is essential for ecological function but is challenging to measure and often relegated to simple metrics such as rugosity. Recent advances in computer vision and machine learning offer the potential to alleviate some of these limitations. We developed an approach to automatically classify 3D reconstructions of reef sections and assessed the accuracy of this approach. 3D reconstructions of reef sections were generated using commercial Structure-from-Motion software with images extracted from video surveys. To generate a 3D classified map, locations on the 3D reconstruction were mapped back into the original images to extract multiple views of the location. Several approaches were tested to merge information from multiple views of a point into a single classification, all of which used convolutional neural networks to classify or extract features from the images, but differ in the strategy employed for merging information. Approaches to merging information entailed voting, probability averaging, and a learned neural-network layer. All approaches performed similarly achieving overall classification accuracies of ~96% and >90% accuracy on most classes. With this high classification accuracy, these approaches are suitable for many ecological applications.This study was funded by grants from the Alfred P. Sloan Foundation (BMH, BR2014-049; https://sloan.org), and the National Science Foundation (MHL, OCE-1657727; https://www.nsf.gov). The funders had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript
WordFences: Text localization and recognition
En col·laboració amb la Universitat de Barcelona (UB) i la Universitat Rovira i Virgili (URV)In recent years, text recognition has achieved remarkable success in recognizing scanned
document text. However, word recognition in natural images is still an open problem,
which generally requires time consuming post-processing steps. We present a novel architecture
for individual word detection in scene images based on semantic segmentation.
Our contributions are twofold: the concept of WordFence, which detects border areas
surrounding each individual word and a unique pixelwise weighted softmax loss function
which penalizes background and emphasizes small text regions. WordFence ensures that
each word is detected individually, and the new loss function provides a strong training
signal to both text and word border localization. The proposed technique avoids intensive
post-processing by combining semantic word segmentation with a voting scheme
for merging segmentations of multiple scales, producing an end-to-end word detection
system. We achieve superior localization recall on common benchmark datasets - 92%
recall on ICDAR11 and ICDAR13 and 63% recall on SVT. Furthermore, end-to-end
word recognition achieves state-of-the-art 86% F-Score on ICDAR13
Multi-branch Convolutional Neural Network for Multiple Sclerosis Lesion Segmentation
In this paper, we present an automated approach for segmenting multiple
sclerosis (MS) lesions from multi-modal brain magnetic resonance images. Our
method is based on a deep end-to-end 2D convolutional neural network (CNN) for
slice-based segmentation of 3D volumetric data. The proposed CNN includes a
multi-branch downsampling path, which enables the network to encode information
from multiple modalities separately. Multi-scale feature fusion blocks are
proposed to combine feature maps from different modalities at different stages
of the network. Then, multi-scale feature upsampling blocks are introduced to
upsize combined feature maps to leverage information from lesion shape and
location. We trained and tested the proposed model using orthogonal plane
orientations of each 3D modality to exploit the contextual information in all
directions. The proposed pipeline is evaluated on two different datasets: a
private dataset including 37 MS patients and a publicly available dataset known
as the ISBI 2015 longitudinal MS lesion segmentation challenge dataset,
consisting of 14 MS patients. Considering the ISBI challenge, at the time of
submission, our method was amongst the top performing solutions. On the private
dataset, using the same array of performance metrics as in the ISBI challenge,
the proposed approach shows high improvements in MS lesion segmentation
compared with other publicly available tools.Comment: This paper has been accepted for publication in NeuroImag
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
Comparative evaluation of instrument segmentation and tracking methods in minimally invasive surgery
Intraoperative segmentation and tracking of minimally invasive instruments is
a prerequisite for computer- and robotic-assisted surgery. Since additional
hardware like tracking systems or the robot encoders are cumbersome and lack
accuracy, surgical vision is evolving as promising techniques to segment and
track the instruments using only the endoscopic images. However, what is
missing so far are common image data sets for consistent evaluation and
benchmarking of algorithms against each other. The paper presents a comparative
validation study of different vision-based methods for instrument segmentation
and tracking in the context of robotic as well as conventional laparoscopic
surgery. The contribution of the paper is twofold: we introduce a comprehensive
validation data set that was provided to the study participants and present the
results of the comparative validation study. Based on the results of the
validation study, we arrive at the conclusion that modern deep learning
approaches outperform other methods in instrument segmentation tasks, but the
results are still not perfect. Furthermore, we show that merging results from
different methods actually significantly increases accuracy in comparison to
the best stand-alone method. On the other hand, the results of the instrument
tracking task show that this is still an open challenge, especially during
challenging scenarios in conventional laparoscopic surgery
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