Seeing the wood for the trees: towards improved quantification of glial cells in central nervous system tissue

The following mini-review attempts to guide researchers in the quantification of fluorescently-labelled proteins within cultured thick or chromogenically-stained proteins within thin sections of brain tissue. It follows from our examination of the utility of Fiji ImageJ thresholding and binarization...

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Vydáno v:Neural regeneration research Ročník 13; číslo 9; s. 1520 - 1523
Hlavní autoři: Healy, Sinéad, McMahon, Jill, FitzGerald, Una
Médium: Journal Article
Jazyk:angličtina
Vydáno: India Wolters Kluwer India Pvt. Ltd 01.09.2018
Medknow Publications and Media Pvt. Ltd
Medknow Publications & Media Pvt. Ltd
Galway Neuroscience Centre, School of Natural Sciences, National University of Ireland, Galway, Ireland
Medknow Publications & Media Pvt Ltd
Wolters Kluwer Medknow Publications
Témata:
Accuracy
Algorithms
Brain research
Fluorescent proteins
Medical research
Neuroglia
Neuroimaging
organotypic brain slice culture; glial cell quantification; thresholding algorithms; Fiji ImageJ; BioVoxxel plug-in; stereology
Performance evaluation
Protein expression
Proteins
Quality
Researchers
Review
Variance analysis
Fiji
glial cell quantification
stereology
BioVoxxel plug-in
Fiji ImageJ
organotypic brain slice culture
thresholding algorithms
ISSN:1673-5374, 1876-7958
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Shrnutí:The following mini-review attempts to guide researchers in the quantification of fluorescently-labelled proteins within cultured thick or chromogenically-stained proteins within thin sections of brain tissue. It follows from our examination of the utility of Fiji ImageJ thresholding and binarization algorithms. Describing how we identified the maximum intensity projection as the best of six tested for two dimensional (2D)-rendering of three-dimensional (3D) images derived from a series of z-stacked micrographs, the review summarises our comparison of 16 global and 9 local algorithms for their ability to accurately quantify the expression of astrocytic glial fibrillary acidic protein (GFAP), microglial ionized calcium binding adapter molecule 1 (IBA1) and oligodendrocyte lineage Olig2 within fixed cultured rat hippocampal brain slices. The application of these algorithms to chromogenically-stained GFAP and IBA1 within thin tissue sections, is also described. Fiji's BioVoxxel plugin allowed categorisation of algorithms according to their sensitivity, specificity accuracy and relative quality. The Percentile algorithm was deemed best for quantifying levels of GFAP, the Li algorithm was best when quantifying IBA expression, while the Otsu algorithm was optimum for Olig2 staining, albeit with over-quantification of oligodendrocyte number when compared to a stereological approach. Also, GFAP and IBA expression in 3,3′-diaminobenzidine (DAB)/haematoxylin-stained cerebellar tissue was best quantified with Default, Isodata and Moments algorithms. The workflow presented in [Figure 1] could help to improve the quality of research outcomes that are based on the quantification of protein with brain tissue.
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Author contributions: SH and UF wrote the manuscript. JM produced the figure.
ISSN:1673-5374
1876-7958
DOI:10.4103/1673-5374.235222