title: Blind image analysis for the compositional and structural characterization of plant cell walls.
abstract: A new image analysis strategy is introduced to determine the composition and the structural characteristics of plant cell walls by combining Raman microspectroscopy and unsupervised data mining methods. The proposed method consists of three main steps: spectral preprocessing, spatial clustering of the image and finally estimation of spectral profiles of pure components and their weights. Point spectra of Raman maps of cell walls were preprocessed to remove noise and fluorescence contributions and compressed with PCA. Processed spectra were then subjected to k-means clustering to identify spatial segregations in the images. Cell wall images were reconstructed with cluster identities and each cluster was represented by the average spectrum of all the pixels in the cluster. Pure components spectra were estimated by spectral entropy minimization criteria with simulated annealing optimization. Two pure spectral estimates that represent lignin and carbohydrates were recovered and their spatial distributions were calculated. Our approach partitioned the cell walls into many sublayers, based on their composition, thus enabling composition analysis at subcellular levels. It also overcame the well known problem that native lignin spectra in lignocellulosics have high spectral overlap with contributions from cellulose and hemicelluloses, thus opening up new avenues for microanalyses of monolignol composition of native lignin and carbohydrates without chemical or mechanical extraction of the cell wall materials.
authors.affiliation: Energy Biosciences Institute, University of California, Berkeley, CA 94720, USA. pperera@berkeley.edu
authors.forename: Pradeep N
authors.initials: PN
authors.lastname: Perera
authors.forename: Martin
authors.initials: M
authors.lastname: Schmidt
authors.forename: P James
authors.initials: PJ
authors.lastname: Schuck
authors.forename: Paul D
authors.initials: PD
authors.lastname: Adams
mesh_terms: D018533:Biomass; D002473:Cell Wall / Q000737:chemistry / Q000378:metabolism / Q000648:ultrastructure; D006801:Humans; D007091:Image Processing, Computer-Assisted / Q000379:methods; D008031:Lignin / Q000737:chemistry / Q000378:metabolism*; D010944:Plants / Q000737:chemistry* / Q000378:metabolism; D011134:Polysaccharides / Q000737:chemistry / Q000378:metabolism; D013059:Spectrum Analysis, Raman / Q000379:methods*
chemical_list: D011134:Polysaccharides; D008031:Lignin