Environmental microorganism classification using conditional random fields and deep convolutional neural networks

Sergey Kosov*, Kimiaki Shirahama, Chen Li, Marcin Grzegorzek

*Corresponding author for this work
5 Citations (Scopus)

Abstract

The labeling of Environmental Microorganisms (EM) which help decomposing pollutants, plays a fundamental role for establishing sustainable ecosystem. We propose an environmental microorganism classification engine that can automatically analyze microscopic images using Conditional Random Fields (CRF) and Deep Convolutional Neural Networks (DCNN). First, to effectively represent scarce training images, a DCNN pre-trained for image classification using a large amount of data is re-purposed to our feature extractor that distils pixel-level features in microscopic images. In addition, pixel-level classification results by such features can be refined using global features that describe the whole image in toto. Finally, our CRF model localizes and classifies EMs by considering the spatial relations among DCNN-based features, and their relations to global features. The experimental results have shown 94.2% of overall segmentation accuracy and up to 91.4% mean average precision of the results.

Original languageEnglish
JournalPattern Recognition
Volume77
Pages (from-to)248-261
Number of pages14
ISSN0031-3203
DOIs
Publication statusPublished - 01.05.2018

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