Semi-automated counting model for arbuscular mycorrhizal fungi spores using the Circle Hough Transform and an artificial neural network.

Clênia A.O De Melo,Alexsandra O Andrade,Juliane G Lopes,Robson S Magalhães,Roque M.P Trindade

doi:10.1590/0001-3765201920180165

Abstract

Arbuscular Mycorrhizae (AM) are mutualistic associations between Arbuscular Mycorrhizal Fungi (AMF) and the roots of many plant species. AMF spores give rise to filaments that develop in the root system of plants and contribute to the absorption of water and some nutrients. This article introduces a semi-automated counting model of AMF spores in slide images based on Artificial Neural Network (ANN). The semi-automated counting of AMF spores facilitates and accelerates the tasks of researchers, who still do the AMF spore counting manually. We built a representative database of spore images, processing images through the Circle Hough Transform (CHT) method and training an ANN to classify patterns automatically. The classification analysis and the performances of the proposed method against the manual method are presented in this paper. The accuracy for the identification of spores by CHT in conjunction to ANN classification in the images was 90%. The results indicate that this method can accurately detect the presence of AMF spores in images as well as count them with a high level of confidence.

Highlights

Arbuscular mycorrhizal fungi (AMF) colonize the roots of the majority of terrestrial plants (Smith and Read 1997)
The patterns of possible spores located by Circle Hough Transform (CHT) in the original image are cut into sub-images and some of the sub-images are resized by standardizing the data that will feed the Artificial Neural Network (ANN)
In the test set (475 patterns) of the 350 spores detected by the expert as “target 1”, the SDIC correctly classified 321 patterns as “target 1”, and 29 patterns as “target 0”, false negative ones (FN)

Summary

Introduction

Arbuscular mycorrhizal fungi (AMF) colonize the roots of the majority of terrestrial plants (Smith and Read 1997). Mycorrhizal colonization is linked to the genotype of the plant and fungi, as well as the environment and diversity. The fact that many species interact with AMF shows the great importance of mycorrhizae for the preservation of flora and this stimulates increasing research on mycorrhizae (Smith and Read 1997). Spores are reproductive structures of an asexual nature and they have a wide structural diversity (Goto and Maia 2006). These structures have varied characteristics, such as the number of layers and appearance, as well as color and wall thickness (Morton 1988). They measure from 22 to 1,050 μm (Schenck and Perez 1990, Schüßler et al 1994)

Methods

Results

Conclusion