TABLE 1.

Fluorescent labels for IRF.

Label name	Demonstrated for	Highlighting	Application		References
			In the freeze-substitution	On-section labeling
Non-specific labels
1.8 ANS	Mammalian tissue	Collagen and/or elastic fibers	✓		Biel et al. (2003)
Acridine orange	Mammalian tissue	Nuclei, cytoplasm	✓		Biel et al. (2003)
	Cultured cells, bacteria	Cytoplasm, nuclei	✓		Lucas et al. (2012)
Bodipy 560	Mammalian tissue	Nuclei, cell membranes	✓		Biel et al. (2003)
DCVJ	Mammalian tissue	Nuclei, collagen and/or elastic fibers	✓		Biel et al. (2003)
DiD	Mammalian tissue	Lipophilic domains, cell membranes	✓		Biel et al. (2003)
	Cultured cells	Lipophilic domains, cell membranes	✓		Lucas et al. (2012)
DiIC18	Mammalian tissue	Lipophilic domains, cell membranes	✓		Biel et al. (2003)
	Cultured cells	Cell membranes	✓		Lucas et al. (2012)
DiOC6	Mammalian tissue	Cytoplasm (lipophilic domains)	✓		Biel et al. (2003)
Nile blue sulfate	Mammalian tissue	Nuclei, cytoplasm, collagen, elastic fibers	✓		Biel et al. (2003)
	Model organisms, e.g., C. elegans	Cytoplasm, cell membranes	✓		Lucas et al. (2012)
	Cultured cells	Nuclei, cytoplasm, cytoskeleton*	✓		Lucas et al. (2012)
Nile red	Cultured cells	Nuclei, cytoplasm	✓		Lucas et al. (2012)
Oregon Green	Mammalian tissue	Nuclei, collagen, elastic fibers	✓		Biel et al. (2003)
Safranin O	Mammalian tissue	Nuclei, cytoplasm, collagen, elastic fibres	✓		Biel et al. (2003)
	Cultured cells	Nuclei, cytoplasm	✓		Lucas et al. (2012)
	Model organisms, e.g., C. elegans	Nuclei, cytoplasm, cell membranes	✓		Lucas et al. (2012)
	Plant tissue	Entire tissue, unspecific	✓		Lucas et al. (2012)
Syto 24	Cultured cells	Entire cell, unspecific	✓		Lucas et al. (2012)
Syto 83	Cultured cells	Entire cell, unspecific	✓		Lucas et al. (2012)
Sytox Green	Cultured cells	Entire cell incl. membranes, unspecific	✓		Lucas et al. (2012)
Tannin	Mammalian tissue	Nuclei	✓		Biel et al. (2003)
Uranyl acetate	Any type of biological specimen	Entire tissue or cell	✓	✓ Note the temperature dependency!	(Biel et al., 2003; Tuijtel et al., 2017)
Specific labels
Dapi	Any type of biological specimen	Nuclei		✓
Hoechst	Any type of biological specimen	Nuclei		✓	Delevoye et al. (2016)
Phalloidin Alexa 488	Cultured cells and mammalian tissue	Cytoskeleton	✓		Lucas et al. (2012)
Genetically encoded tags
	Standard IRF	Super-resolution LM	References
Citrine	✓		Watanabe et al. (2011)
GFP/mGFP	✓	✓	(van Rijnsoever et al., 2008; Nixon et al., 2009; Kukulski et al., 2011; Johnson et al., 2015; Delevoye et al., 2016; Bissig et al., 2017; Peddie et al., 2017; Burel et al., 2018; Ripoll et al., 2018)
mCherry	✓	✓	(Höhn et al., 2015; Ripoll et al., 2018)
mEos-derivatives		✓	(Watanabe et al., 2011; Paez-Segala et al., 2015; Kopek et al., 2017; Fu et al., 2020)
mRuby2		✓	Johnson et al. (2015)
mVenus		✓	Johnson et al. (2015)
YFP	✓		(Heiligenstein et al., 2014; Delevoye et al., 2016)

Table adapted from Lucas et al. (2012) with permission of Elsevier Ltd.