Jacobus J Barnard

Abstract:

We present an algorithm which uses information from both surface reflectance and illumination variation to solve for color constancy. Most color constancy algorithms assume that the illumination across a scene is constant, but this is very often not valid for real images. The method presented in this work identifies and removes the illumination variation, and in addition uses the variation to constrain the solution. The constraint is applied conjunctively to constraints found from surface reflectances. Thus the algorithm can provide good color constancy when there is sufficient variation in surface reflectances, or sufficient illumination variation, or a combination of both. We present the results of running the algorithm on several real scenes, and the results are very encouraging. © 1997 Academic Press.

Abstract:

Illumination is rarely constant in intensity or color throughout a scene. Multiple light sources with different spectra - sun and sky, direct and interreflected light - are the norm. Nonetheless, almost all color constancy algorithms assume that the spectrum of the incident illumination remains constant across the scene. We assume the converse, that illumination does vary, in developing a new algorithm for color constancy. Rather than creating difficulties, varying illumination is in fact a very powerful constraint. Indeed tests of our algorithm using real images of an office scene show excellent results.

PMID: 18551166;PMCID: PMC2396484;Abstract:

Genetic variation on the non-recombining portion of the Y chromosome contains information about the ancestry of male lineages. Because of their low rate of mutation, single nucleotide polymorphisms (SNPs) are the markers of choice for unambiguously classifying Y chromosomes into related sets of lineages known as haplogroups, which tend to show geographic structure in many parts of the world. However, performing the large number of SNP genotyping tests needed to properly infer haplogroup status is expensive and time consuming. A novel alternative for assigning a sampled Y chromosome to a haplogroup is presented here. We show that by applying modern machine-learning algorithms we can infer with high accuracy the proper Y chromosome haplogroup of a sample by scoring a relatively small number of Y-linked short tandem repeats (STRs). Learning is based on a diverse ground-truth data set comprising pairs of SNP test results (haplogroup) and corresponding STR scores. We apply several independent machine-learning methods in tandem to learn formal classification functions. The result is an integrated high-throughput analysis system that automatically classifies large numbers of samples into haplogroups in a cost-effective and accurate manner. © 2008 Schlecht et al.

doi: 10.1109/CVPR.2011.5995736

PMID: 22036294;Abstract:

Alternaria is one of the most cosmopolitan fungal genera encountered and impacts humans and human activities in areas of material degradation, phytopathology, food toxicology, and respiratory disease. Contemporary methods of taxon identification rely on assessments of morphology related to sporulation, which are critical for accurate diagnostics. However, the morphology of Alternaria is quite complex, and precise characterization can be laborious, time-consuming, and often restricted to experts in this field. To make morphology characterization easier and more broadly accessible, a generalized statistical model was developed for the three-dimensional geometric structure of the sporulation apparatus. The model is inspired by the widely used grammar-based models for plants, Lindenmayer-systems, which build structure by repeated application of rules for growth. Adjusting the parameters of the underlying probability distributions yields variations in the morphology, and thus the approach provides an excellent tool for exploring the morphology of Alternaria under different assumptions, as well as understanding how it is largely the consequence of local rules for growth. Further, different choices of parameters lead to different model groups, which can then be visually compared to published descriptions or microscopy images to validate parameters for species-specific models. The approach supports automated analysis, as the models can be fit to image data using statistical inference, and the explicit representation of the geometry allows the accurate computation of any morphological quantity. Furthermore, because the model can encode the statistical variation of geometric parameters for different species, it will allow automated species identification from microscopy images using statistical inference. In summary, the approach supports visualization of morphology, automated quantification of phenotype structure, and identification based on form. © 2011 British Mycological Society.