A workflow for low-cost automated image analysis of myxomycete spore numbers, size and shape.
Computer vision
Particle analysis
Physarum albescens
Size distribution
Spore diameter
Spore shape
Journal
PeerJ
ISSN: 2167-8359
Titre abrégé: PeerJ
Pays: United States
ID NLM: 101603425
Informations de publication
Date de publication:
2021
2021
Historique:
received:
16
11
2020
accepted:
20
10
2021
entrez:
25
11
2021
pubmed:
26
11
2021
medline:
26
11
2021
Statut:
epublish
Résumé
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
Identifiants
pubmed: 34820196
doi: 10.7717/peerj.12471
pii: 12471
pmc: PMC8605758
doi:
Types de publication
Journal Article
Langues
eng
Pagination
e12471Informations de copyright
©2021 Woyzichovski et al.
Déclaration de conflit d'intérêts
The authors declare there are no competing interests.
Références
Protist. 2020 Dec;171(6):125771
pubmed: 33171353
ISME J. 2018 Aug;12(8):2051-2060
pubmed: 29849168
MethodsX. 2016 Mar 17;3:231-41
pubmed: 27073786
Nat Methods. 2019 Dec;16(12):1226-1232
pubmed: 31570887
PLoS One. 2017 Apr 17;12(4):e0174825
pubmed: 28414791
Curr Genet. 2017 Oct;63(5):831-838
pubmed: 28421279
Mycologia. 2013 Nov-Dec;105(6):1535-46
pubmed: 23921236
Ecology. 2014 Jun;95(6):1612-21
pubmed: 25039225
Plant Biol (Stuttg). 2014 Mar;16(2):508-11
pubmed: 24341784
Light Sci Appl. 2018 Sep 19;7:66
pubmed: 30245813
Naturwissenschaften. 2009 Jan;96(1):147-51
pubmed: 18836695
Bioinformatics. 2017 Aug 1;33(15):2424-2426
pubmed: 28369169
Methods Mol Biol. 2019;1992:307-322
pubmed: 31148047
PLoS Comput Biol. 2019 Oct 31;15(10):e1007428
pubmed: 31671091
Protist. 2016 Aug;167(4):319-338
pubmed: 27351595
Mycologia. 2009 Jan-Feb;101(1):1-16
pubmed: 19271666
Protist. 2016 Jun;167(3):234-53
pubmed: 27128786
Mycologia. 2006 Mar-Apr;98(2):223-32
pubmed: 16894967
Nat Methods. 2012 Jun 28;9(7):676-82
pubmed: 22743772
Mycol Res. 2008 Jun;112(Pt 6):697-707
pubmed: 18495452