Method	Staining or Autofluorescence	Purpose	Species or Material Analyzed	Reference
CLSM	BODIPY, ovalbumin with fluorescein	Lignin peroxidase effectiveness	Lignin peroxidases	[79]
CLSM	Autofluorescence, monolignol fluorescence	Lignin transport and polymerization	Arabidopsis thaliana	[81,82,83]
CLSM	Monolignol fluorescence	Lignin polymerization	Arabidopsis thaliana, Pinus radiata	[85]
CLSM	Autofluorescence, monolignol fluorescence	Lignin polymerization	Linum usitatissimum	[86]
CLSM	Basic Fuchsin, Aramine O, Direct Yellow 96	Protocol for staining cell walls	Arabidopsis thaliana	[73]
CLSM	Basic Fuchsin	Lignin distribution	Brachypodium distachyon	[74]
CLSM	Monolignol fluorescence	Lignin polymerization	Arabidopsis thaliana	[84]
CLSM	Autofluorescence	Recalcitrant biomass	Miscanthus, poplar, wheat straw	[77]
CLSM	Autofluorescence	Lignin distribution	Arabidopsis thaliana	[68]
CLSM	Autofluorescence	Protocol for lignin fluorescence intensity	Acacia melanoxylon, Eucalyptus nitens, Pinus radiata, Populus deltoides, P. heterophylla, Salix chilensis, and S. nigra	[39]
CLSM	Autofluorescence	Wood characterization and lignin distribution	Pinus radiata	[70]
CLSM	Safranin	Safranin staining protocol and lignin distribution	Pinus radiata, Populus deltoides, Pseudotsuga menziesii	[53]
CLSM	Autofluorescence	Lignin concentration	Arabidopsis thaliana, Linum usitatissimum, Populus tremula × alba, Zea mays	[69]
CLSM	Autofluorescence	Presence of lignin in cellulose nanofibers	Poplar powder	[75]
CLSM	Autofluorescence, phloroglucinol	Presence of fluorophores in pine leaves	Pinus radiata needles	[41]
CLSM	Autofluorescence	Archaeological wood degradation	Fir wood	[72]
CLSM	p-HTEA solution	New biomass staining protocol	Lignocellulosic biomass	[71]
CLSM	Autofluorescence, monolignol fluorescence	Dual labeling protocol for lignin	Linum usitatissimum	[83]
CLSM	Autofluorescence	Structural changes due to heat treatments	Populus cathayana	[78]
CLSM	Basic Fuchsin, Aramine O, calcofluor white	Laccases lignin polymerization	Arabidopsis thaliana	[87]
CLSM, FLIM	Autofluorescence	Comparison between normal and compression wood	Pinus radiata	[89]
CLSM, FLIM	Autofluorescence	Lignin characterization	Arabidopsis thaliana	[90]
CLSM, FLIM	Autofluorescence	Presence of lignin in cellulose nanofibers	Nanocellulose fibers	[38]
CLSM, FLIM, Epi	Acridine orange	Fungal oxidation of wood	White spruce sapwood	[94]
CLSM, FLIM, FRET	Autofluorescence, Rhodamine B	Saccharification treatments	Pine, poplar coppice	[25]
CLSM, FLIM, TPM	Autofluorescence	Saccharification treatments	Miscanthus × giganteus, poplar, wheat straw	[43]
CLSM, FLIM, TPM	Autofluorescence	Alkaline and acid treatments for lignin	Eucalyptus fibers, sugarcane bagasse	[92]
CLSM, FLIM, TPM	Autofluorescence	Characterization of lignocellulosic biomass	Sugarcane bagasse	[93]
CLSM, FRAP	Autofluorescence, PEG-rhodamine	Saccharification treatments	Populus nigra × deltoides	[25]
CLSM, FRAP	Autofluorescence and probes	Diffusion of probes and FRAP effectiveness	Feruloylated arabinoxylan gels	[106]
CLSM, FRET	FITC, Rhodamine B	Lignin nanoparticles with peroxidases and laccases	Lignin nanoparticles	[66]
CLSM, FRET	Autofluorescence and PEG-rhodamine	Interaction between PEG and recalcitrant lignin	Pinus radiata	[67]
CLSM, FRET	Autofluorescence and Congo red	Lignin recalcitrance	Pinus	[80]
CLSM, FRET, SLIM	Autofluorescence and Rhodamine B	Probe effectiveness	Wheat straw	[97]
CLSM, STED	PEG-rhodamine (PEG-R)	Method Comparison	Poplar	[109]
CLSM, TIRF, Epi	Calcofluor white	Fiber characterization	Agave fibers, garlic skin	[108]
CLSM, TPM	Autofluorescence	Changes in wood	Spruce	[101]
Epi	Autofluorescence, safranin	Lignin distribution	Fraxinus ornus, Myrtus communis, Olea europaea, Pistacia lentiscus, Rhamnus alaternus	[36]
Epi	Safranin/fast green	Characterization of secondary xylem lignin	34 species of Cactaceae	[62]
Epi	Safranin/fast green	Characterization of primary xylem lignin	8 species of Cactaceae	[115]
Epi	Autofluorescence	Lignin distribution	Pinus yunnanensis	[59]
Epi	Modified Mäule staining	Staining protocol	Betula platyphylla	[61]
Epi	Autofluorescence	Structural changes due to heat treatments	Fraxinus excelsior	[60]
Epi	Safranin	Fungal degradation of wood	Eucalyptus grandis	[64]
Epi	Acriflavine	Lignocellulose distribution	Cannabis sativa	[58]
Epi, CLSM	Autofluorescence, Filipin fluorescent antibiotic reacting	Biopulping with fungus	Eucalyptus globulus	[76]
Epi, CLSM	Autofluorescence, Congo red, Fluorol yellow	Protocol for analyzing cell walls	Bruguiera gymnorrhiza, Picea glauca, Pinus ponderosa, Populus tremuloides, Rhizophora apiculata	[57]
Epi, FLIM, TPM	Autofluorescence	Biomass morphological changes due to hydrolysis	Corn stover	[55]
Epi, FRAP	Autofluorescence, m-CHERRY red protein	Lignin polymerization	Arabidopsis	[104]
Epi, FRET	Synthesized fluorochromes	Lignin polymerization	Artificial lignified maize cell walls	[44]
FLIM	Autofluorescence	Protocol to identify timber species	Beech, maple, spruce, and walnut	[95]
FLIM	Autofluorescence	Lignin composition	Arabidopsis thaliana	[96]
TPM	Autofluorescence	Structure analysis of chitosan-lignin film	Chitosan-lignin composite film	[102]
TPM, FRAP, FRET, sFLIM	Autofluorescence	Protocol to analyze biomass	Wheat straw	[103]