AxonDeepSeg: automatic axon and myelin segmentation from microscopy data using convolutional neural networks

Segmentation of axon and myelin from microscopy images of the nervous system provides useful quantitative information about the tissue microstructure, such as axon density and myelin thickness. This could be used for instance to document cell morphometry across species, or to validate novel non-invasive quantitative magnetic resonance imaging techniques. Most currently-available segmentation algorithms are based on standard image processing and usually require multiple processing steps and/or parameter tuning by the user to adapt to different modalities. Moreover, only few methods are publicly available. We introduce AxonDeepSeg, an open-source software that performs axon and myelin segmentation of microscopic images using deep learning. AxonDeepSeg features: (i) a convolutional neural network architecture; (ii) an easy training procedure to generate new models based on manually-labelled data and (iii) two ready-to-use models trained from scanning electron microscopy (SEM) and transmission electron microscopy (TEM). Results show high pixel-wise accuracy across various species: 85% on rat SEM, 81% on human SEM, 95% on mice TEM and 84% on macaque TEM. Segmentation of a full rat spinal cord slice is computed and morphological metrics are extracted and compared against the literature. AxonDeepSeg is freely available at https://github.com/neuropoly/axondeepsegComment: 14 pages, 7 figure

Potato Classification Using Deep Learning

Abstract: Potatoes are edible tubers, available worldwide and all year long. They are relatively cheap to grow, rich in nutrients, and they can make a delicious treat. The humble potato has fallen in popularity in recent years, due to the interest in low-carb foods. However, the fiber, vitamins, minerals, and phytochemicals it provides can help ward off disease and benefit human health. They are an important staple food in many countries around the world. There are an estimated 200 varieties of potatoes, which can be classified into a number of categories based on the cooked texture and ingredient functionality. Using a public dataset of 2400 images of potatoes, we trained a deep convolutional neural network to identify 4 types (Red, Red Washed, Sweet, and White).The trained model achieved an accuracy of 99.5% of test set, demonstrating the feasibility of this approach

A Deep Learning Approach to Denoise Optical Coherence Tomography Images of the Optic Nerve Head

Purpose: To develop a deep learning approach to de-noise optical coherence tomography (OCT) B-scans of the optic nerve head (ONH). Methods: Volume scans consisting of 97 horizontal B-scans were acquired through the center of the ONH using a commercial OCT device (Spectralis) for both eyes of 20 subjects. For each eye, single-frame (without signal averaging), and multi-frame (75x signal averaging) volume scans were obtained. A custom deep learning network was then designed and trained with 2,328 "clean B-scans" (multi-frame B-scans), and their corresponding "noisy B-scans" (clean B-scans + gaussian noise) to de-noise the single-frame B-scans. The performance of the de-noising algorithm was assessed qualitatively, and quantitatively on 1,552 B-scans using the signal to noise ratio (SNR), contrast to noise ratio (CNR), and mean structural similarity index metrics (MSSIM). Results: The proposed algorithm successfully denoised unseen single-frame OCT B-scans. The denoised B-scans were qualitatively similar to their corresponding multi-frame B-scans, with enhanced visibility of the ONH tissues. The mean SNR increased from $4.02 \pm 0.68$ dB (single-frame) to $8.14 \pm 1.03$ dB (denoised). For all the ONH tissues, the mean CNR increased from $3.50 \pm 0.56$ (single-frame) to $7.63 \pm 1.81$ (denoised). The MSSIM increased from $0.13 \pm 0.02$ (single frame) to $0.65 \pm 0.03$ (denoised) when compared with the corresponding multi-frame B-scans. Conclusions: Our deep learning algorithm can denoise a single-frame OCT B-scan of the ONH in under 20 ms, thus offering a framework to obtain superior quality OCT B-scans with reduced scanning times and minimal patient discomfort

A General Theory of Equivariant CNNs on Homogeneous Spaces

We present a general theory of Group equivariant Convolutional Neural Networks (G-CNNs) on homogeneous spaces such as Euclidean space and the sphere. Feature maps in these networks represent fields on a homogeneous base space, and layers are equivariant maps between spaces of fields. The theory enables a systematic classification of all existing G-CNNs in terms of their symmetry group, base space, and field type. We also consider a fundamental question: what is the most general kind of equivariant linear map between feature spaces (fields) of given types? Following Mackey, we show that such maps correspond one-to-one with convolutions using equivariant kernels, and characterize the space of such kernels

A Convolutional Neural Network for the Automatic Diagnosis of Collagen VI related Muscular Dystrophies

The development of machine learning systems for the diagnosis of rare diseases is challenging mainly due the lack of data to study them. Despite this challenge, this paper proposes a system for the Computer Aided Diagnosis (CAD) of low-prevalence, congenital muscular dystrophies from confocal microscopy images. The proposed CAD system relies on a Convolutional Neural Network (CNN) which performs an independent classification for non-overlapping patches tiling the input image, and generates an overall decision summarizing the individual decisions for the patches on the query image. This decision scheme points to the possibly problematic areas in the input images and provides a global quantitative evaluation of the state of the patients, which is fundamental for diagnosis and to monitor the efficiency of therapies.Comment: Submitted for review to Expert Systems With Application