A workflow for low-cost automated image analysis of myxomycete spore numbers, size and shape

Measuring spore size is a standard method for the description of fungal taxa, but in manual microscopic analyses the number of spores that can be measured and information on their morphological traits are typically limited. To overcome this weakness we present a method to analyze the size and shape...

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Autores principales:	Jan Woyzichovski, Oleg Shchepin, Nikki Heherson Dagamac, Martin Schnittler
Formato:	article
Lenguaje:	EN
Publicado:	PeerJ Inc. 2021
Materias:	Particle analysis Physarum albescens Size distribution Spore diameter Computer vision Spore shape Medicine R
Acceso en línea:	https://doaj.org/article/76dc4895721045838318a019bf493f2d
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spelling	oai:doaj.org-article:76dc4895721045838318a019bf493f2d2021-11-18T15:05:35ZA workflow for low-cost automated image analysis of myxomycete spore numbers, size and shape10.7717/peerj.124712167-8359https://doaj.org/article/76dc4895721045838318a019bf493f2d2021-11-01T00:00:00Zhttps://peerj.com/articles/12471.pdfhttps://peerj.com/articles/12471/https://doaj.org/toc/2167-8359Measuring spore size is a standard method for the description of fungal taxa, but in manual microscopic analyses the number of spores that can be measured and information on their morphological traits are typically limited. To overcome this weakness we present a method to analyze the size and shape of large numbers of spherical bodies, such as spores or pollen, by using inexpensive equipment. A spore suspension mounted on a slide is treated with a low-cost, high-vibration device to distribute spores uniformly in a single layer without overlap. Subsequently, 10,000 to 50,000 objects per slide are measured by automated image analysis. The workflow involves (1) slide preparation, (2) automated image acquisition by light microscopy, (3) filtering to separate high-density clusters, (4) image segmentation by applying a machine learning software, Waikato Environment for Knowledge Analysis (WEKA), and (5) statistical evaluation of the results. The technique produced consistent results and compared favorably with manual measurements in terms of precision. Moreover, measuring spore size distribution yields information not obtained by manual microscopic analyses, as shown for the myxomycete Physarum albescens. The exact size distribution of spores revealed irregularities in spore formation resulting from the influence of environmental conditions on spore maturation. A comparison of the spore size distribution within and between sporocarp colonies showed large environmental and likely genetic variation. In addition, the comparison identified specimens with spores roughly twice the normal size. The successful implementation of the presented method for analyzing myxomycete spores also suggests potential for other applications.Jan WoyzichovskiOleg ShchepinNikki Heherson DagamacMartin SchnittlerPeerJ Inc.articleParticle analysisPhysarum albescensSize distributionSpore diameterComputer visionSpore shapeMedicineRENPeerJ, Vol 9, p e12471 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Particle analysis Physarum albescens Size distribution Spore diameter Computer vision Spore shape Medicine R
spellingShingle	Particle analysis Physarum albescens Size distribution Spore diameter Computer vision Spore shape Medicine R Jan Woyzichovski Oleg Shchepin Nikki Heherson Dagamac Martin Schnittler A workflow for low-cost automated image analysis of myxomycete spore numbers, size and shape
description	Measuring spore size is a standard method for the description of fungal taxa, but in manual microscopic analyses the number of spores that can be measured and information on their morphological traits are typically limited. To overcome this weakness we present a method to analyze the size and shape of large numbers of spherical bodies, such as spores or pollen, by using inexpensive equipment. A spore suspension mounted on a slide is treated with a low-cost, high-vibration device to distribute spores uniformly in a single layer without overlap. Subsequently, 10,000 to 50,000 objects per slide are measured by automated image analysis. The workflow involves (1) slide preparation, (2) automated image acquisition by light microscopy, (3) filtering to separate high-density clusters, (4) image segmentation by applying a machine learning software, Waikato Environment for Knowledge Analysis (WEKA), and (5) statistical evaluation of the results. The technique produced consistent results and compared favorably with manual measurements in terms of precision. Moreover, measuring spore size distribution yields information not obtained by manual microscopic analyses, as shown for the myxomycete Physarum albescens. The exact size distribution of spores revealed irregularities in spore formation resulting from the influence of environmental conditions on spore maturation. A comparison of the spore size distribution within and between sporocarp colonies showed large environmental and likely genetic variation. In addition, the comparison identified specimens with spores roughly twice the normal size. The successful implementation of the presented method for analyzing myxomycete spores also suggests potential for other applications.
format	article
author	Jan Woyzichovski Oleg Shchepin Nikki Heherson Dagamac Martin Schnittler
author_facet	Jan Woyzichovski Oleg Shchepin Nikki Heherson Dagamac Martin Schnittler
author_sort	Jan Woyzichovski
title	A workflow for low-cost automated image analysis of myxomycete spore numbers, size and shape
title_short	A workflow for low-cost automated image analysis of myxomycete spore numbers, size and shape
title_full	A workflow for low-cost automated image analysis of myxomycete spore numbers, size and shape
title_fullStr	A workflow for low-cost automated image analysis of myxomycete spore numbers, size and shape
title_full_unstemmed	A workflow for low-cost automated image analysis of myxomycete spore numbers, size and shape
title_sort	workflow for low-cost automated image analysis of myxomycete spore numbers, size and shape
publisher	PeerJ Inc.
publishDate	2021
url	https://doaj.org/article/76dc4895721045838318a019bf493f2d
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A workflow for low-cost automated image analysis of myxomycete spore numbers, size and shape

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