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

PeerJ

article

Jan Woyzichovski¹  Oleg Shchepin¹  Nikki Heherson Dagamac¹  Martin Schnittler¹ 

[1] Institute of Botany and Landscape Ecology, Greifswald University;Laboratory of Systematics and Geography of Fungi, Komarov Botanical Institute of the Russian Academy of Sciences;Department of Biological Sciences and Research Center for the Natural and Applied Sciences, University of Santo Tomas

关键词: Particle analysis;    Physarum albescens;    Size distribution;    Spore diameter;    Computer vision;    Spore shape;   

DOI  :  10.7717/peerj.12471

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

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.

【 授权许可】

CC BY