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The comparison described in this paper has been motivated by two things: 1) a “spectral library” of shortwave infrared reflectance spectra that we have built, consisting of the spectra of 60 nominally pure materials (mostly minerals, but also water, dry vegetation, and several man-made materials) and 2) the needs of users in the mining industry for the use of fast and accurate unmixing software to analyze tens to hundreds of thousands of spectra measured from drill core or chips using HyLogging instruments, and other commercial reflectance spectrometers. Individual samples are typically a mixture of only one, two, three, or occasionally four minerals. Therefore, in order to avoid overfitting, a sparse unmixing algorithm is required. We compare three such algorithms using some real world test data sets: full subset selection (FSS), sparse demixing (SD), and L1 regularization. To aid the comparison, we introduce two novel aspects: 1) the simultaneous fitting of the low frequency background with mineral identification (which provides greater model flexibility) and 2) the combined fitting being carried out using a suitably defined Mahalanobis distance; this has certain optimality properties under an idealized model. Together, these two innovations significantly improve the accuracy of the results. FSS and L1 regularization (suitably optimized) produce similar levels of accuracy, and are superior to SD. Discussion includes possible improvements to the algorithms, and their possible use in other domains. [ABSTRACT FROM PUBLISHER]

Root architecture traits are a target for pre-breeders. Incorporation of root architecture traits into new cultivars requires phenotyping. It is attractive to rapidly and directly phenotype root architecture in the field, avoiding laboratory studies that may not translate to the field. A combination of soil coring with a hydraulic push press and manual core-break counting can directly phenotype root architecture traits of depth and distribution in the field through to grain development, but large teams of people are required and labour costs are high with this method. We developed a portable fluorescence imaging system (BlueBox) to automate root counting in soil cores with image analysis software directly in the field. The lighting system was optimized to produce high-contrast images of roots emerging from soil cores. The correlation of the measurements with the root length density of the soil cores exceeded the correlation achieved by human operator measurements (R2=0.68 versus 0.57, respectively). A BlueBox-equipped team processed 4.3 cores/hour/person, compared with 3.7 cores/hour/person for the manual method. The portable, automated infield root architecture phenotyping system was 16% more labour efficient, 19% more accurate, and 12% cheaper than manual conventional coring, and presents an opportunity to directly phenotype root architecture in the field as part of pre-breeding programs. The platform has wide possibilities to capture more information about root health and other root traits in the field. [ABSTRACT FROM AUTHOR]

Quantitative grading of opals is a challenging task even for skilled opal assessors. Current opal evaluation practices are highly subjective due to the complexities of opal assessment and the limitations of human visual observation. In this paper, we present a novel machine vision system for the automated grading of opals—the gemological digital analyzer (GDA). The grading is based on statistical machine learning with multiple characteristics extracted from opal images. The assessment workflow includes calibration, opal image capture, image analysis, and opal classification and grading. Experimental results show that the GDA-based grading is more consistent and objective compared with the manual evaluations conducted by the skilled opal assessors. [ABSTRACT FROM PUBLISHER]

Natural variation within species reveals aspects of genome evolution and function. The fission yeast Schizosaccharomyces pombe is an important model for eukaryotic biology, but researchers typically use one standard laboratory strain. To extend the usefulness of this model, we surveyed the genomic and phenotypic variation in 161 natural isolates. We sequenced the genomes of all strains, finding moderate genetic diversity (π = 3 × 10−3 substitutions/site) and weak global population structure. We estimate that dispersal of S. pombe began during human antiquity (∼340 BCE), and ancestors of these strains reached the Americas at ∼1623 CE. We quantified 74 traits, finding substantial heritable phenotypic diversity. We conducted 223 genome-wide association studies, with 89 traits showing at least one association. The most significant variant for each trait explained 22% of the phenotypic variance on average, with indels having larger effects than SNPs. This analysis represents a rich resource to examine genotype-phenotype relationships in a tractable model. [ABSTRACT FROM AUTHOR]

Background: Measuring grain characteristics is an integral component of cereal breeding and research into genetic control of seed development. Measures such as thousand grain weight are fast, but do not give an indication of variation within a sample. Other methods exist for detailed analysis of grain size, but are generally costly and very low throughput. Grain colour analysis is generally difficult to perform with accuracy, and existing methods are expensive and involved. Results: We have developed a software method to measure grain size and colour from images captured with consumer level flatbed scanners, in a robust, standardised way. The accuracy and precision of the method have been demonstrated through screening wheat and Brachypodium distachyon populations for variation in size and colour. Conclusion: By using GrainScan, cheap and fast measurement of grain colour and size will enable plant research programs to gain deeper understanding of material, where limited or no information is currently available. [ABSTRACT FROM AUTHOR]