Type

Journal Article

Authors

Noel E. O'Connor
Alfred Nuttall
Teresa Wilson
Sandra Rugonyi
Kevin McGuinness
Julia Dietlmeier

Subjects

Computer Science

Topics
image processing machine learning algorithms large scale scanning electron microscopy sem state of the art artificial intelligence focused ion beam fib microscopy

Few-shot hypercolumn-based mitochondria segmentation in cardiac and outer hair cells in focused ion beam-scanning electron microscopy (FIB-SEM) data (2020)

Abstract We present a novel AI-based approach to the few-shot automated segmentation of mitochondria in large-scale electron microscopy images. Our framework leverages convolutional features from a pre-trained deep multilayer convolutional neural network, such as VGG-16. We then train a binary gradient boosting classifier on the resulting high-dimensional feature hypercolumns. We extract VGG-16 features from the first four convolutional blocks and apply bilinear upsampling to resize the obtained maps to the input image size. This procedure yields a 2688-dimensional feature hypercolumn for each pixel in a 224 x 224 input image. We then apply L1-regularized logistic regression for supervised active feature selection to reduce dependencies among the features, to reduce overfitting, as well as to speed-up gradient boosting-based training. During inference we block process 1728 x 2022 large microscopy images. Our experiments show that in such a formulation of transfer learning our processing pipeline is able to achieve high-accuracy results on very challenging datasets containing a large number of irregularly shaped mitochondria in cardiac and outer hair cells. Our proposed few-shot training approach gives competitive performance with the state-of-the-art using far less training data.
Collections Ireland -> Dublin City University -> Subject = Computer Science: Artificial intelligence
Ireland -> Dublin City University -> Subject = Computer Science: Image processing
Ireland -> Dublin City University -> Publication Type = Article
Ireland -> Dublin City University -> Status = Published
Ireland -> Dublin City University -> DCU Faculties and Centres = DCU Faculties and Schools: Faculty of Engineering and Computing: School of Electronic Engineering
Ireland -> Dublin City University -> Subject = Computer Science: Algorithms
Ireland -> Dublin City University -> DCU Faculties and Centres = Research Initiatives and Centres: INSIGHT Centre for Data Analytics
Ireland -> Dublin City University -> Subject = Computer Science: Machine learning

Full list of authors on original publication

Noel E. O'Connor, Alfred Nuttall, Teresa Wilson, Sandra Rugonyi, Kevin McGuinness, Julia Dietlmeier

Experts in our system

1
Noel E. O'Connor
Dublin City University
Total Publications: 474
 
2
Kevin McGuinness
Dublin City University
Total Publications: 93
 
3
Julia Dietlmeier
Dublin City University
Total Publications: 9