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Evaluation of the IES Method for Evaluating Light Source Color Rendition in terms of Metamer Mismatching

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2016-11
Abstract: 

The Illumination Engineering Society’s Rf color rendering index [IES TM-30-15, 201] is compared to the MMCRI [Metamer Mismatching as a Measure of the Color Rendering of Lights, Mirzaei & Funt, Proc. AIC 2015]. IES Rf is based on color differences using a special set of 99 surface reflectances; while, in contrast, MMCRI is based on all theoretically possible reflectances. The two indices evaluate many lights similarly, but the MMCRI ranks some lights—especially those having strong peaks and wavelength regions of minimal power—lower than does Rf. Is this difference in rating simply due to the fact that MMCRI uses all theoretically possible reflectances including step functions? A ‘practical’ version of MMCRI based on a set of 41 million real, measured spectral reflectances, rather than all theoretically possible reflectances, turns out to concur with the original MMCRI and shows that the disagreement between Rf and MMCRI is more fundamental. Overall, the present study suggests that Rf may overrate the color rendering properties of some lights; and, at the very least, indicate the type of lights upon which future psychophysical testing should concentrate.

Document type: 
Conference presentation
File(s): 

Camera Color Accuracy Evaluated via Metamer Mismatch Moments

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2017-10
Abstract: 

A novel method for evaluating the colorimetric accuracy of digital color cameras is proposed based on a new measure of metamer mismatch body (MMB) induced by the change from the camera as an observer to the human standard observer. Previous methods of evaluating the colorimetric accuracy of a camera at the Luther condition [1], the mean CIE 

Document type: 
Conference presentation
File(s): 

A Colour Rendering Index for Dichromats

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2017-10
Abstract: 

We propose a method of evaluating the colour rendering quality of light sources tailored to dichromatic vision. To the best of our knowledge, the proposed color rendering index (CRI) is the first such index to be specifically designed for dichromats. Previous CRIs have been defined only for trichromats and they generally rely on measuring ΔE colour differences in a standardized uniform colour space such as CAM02-UCS. Since these spaces are defined only for trichromatic colour vision these methods do not generalize to the case of dichromatic colour vision. The proposed dichromat CRI is based on the metamer mismatch index, which applies to both the trichromatic and dichromatic cases.

Document type: 
Conference presentation
File(s): 

Colorizing Color Images

Author: 
Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2018-02
Abstract: 

This paper describes a method of improving the quality of the color in color images by colorizing them. In particular, color quality may suffer from improper white balance and other factors such as inadequate camera characterization. Colorization generally refers to the problem of turning a luminance image into a realistic looking color image and impressive results have been reported in the computer vision literature. Based on the assumption that if colorization can successfully predict colors from luminance data alone then it should certainly be able to predict colors from color data, the proposed method employs colorization to ‘color’ color images. Tests show that the proposed method quite effectively removes color casts—including spatially varying color casts—created by changes in the illumination. The colorization method itself is based on training a deep neural network to learn the connection between the colors in an improperly balanced image and those in a properly balanced one. Unlike many traditional white-balance methods, the proposed method is image-inimage- out and does not explicitly estimate the chromaticity of the illumination nor apply a von-Kries-type adaptation step. The colorization method is also spatially varying and so handles spatially varying illumination conditions without further modification.

Document type: 
Conference presentation
File(s): 

HUE: The Hourly Usage of Energy Dataset for Buildings in British Columbia

Author: 
Peer reviewed: 
No, item is not peer reviewed.
Date created: 
2018-09-03
Abstract: 

The HUE dataset contains donated data from residential customers of BCHydro, a provincial power utility. There are currently twenty-two houses contain within the dataset with most houses having three years of consumption history. Data is downloaded from BCHydro’s customer web porthole by each customer how donated the data. The porthole only allows customers to download a maximum of three years worth of data. Only BCHydro customers were asked to donate to keep the data quality consistent. Weather data from the nearest weather station is also included.

Document type: 
Technical Report
File(s): 

DIDA: Distributed Indexing Dispatched Alignment

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2015
Abstract: 

One essential application in bioinformatics that is affected by the high-throughput sequencing data deluge is the sequence alignment problem, where nucleotide or amino acid sequences are queried against targets to find regions of close similarity. When queries are too many and/or targets are too large, the alignment process becomes computationally challenging. This is usually addressed by preprocessing techniques, where the queries and/or targets are indexed for easy access while searching for matches. When the target is static, such as in an established reference genome, the cost of indexing is amortized by reusing the generated index. However, when the targets are non-static, such as contigs in the intermediate steps of a de novo assembly process, a new index must be computed for each run. To address such scalability problems, we present DIDA, a novel framework that distributes the indexing and alignment tasks into smaller subtasks over a cluster of compute nodes. It provides a workflow beyond the common practice of embarrassingly parallel implementations. DIDA is a cost-effective, scalable and modular framework for the sequence alignment problem in terms of memory usage and runtime. It can be employed in large-scale alignments to draft genomes and intermediate stages of de novo assembly runs. The DIDA source code, sample files and user manual are available through http://www.bcgsc.ca/platform/bioinfo/software/dida. The software is released under the British Columbia Cancer Agency License (BCCA), and is free for academic use.

Document type: 
Article
File(s): 

Robustness of Massively Parallel Sequencing Platforms

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2015
Abstract: 

The improvements in high throughput sequencing technologies (HTS) made clinical sequencing projects such as ClinSeq and Genomics England feasible. Although there are significant improvements in accuracy and reproducibility of HTS based analyses, the usability of these types of data for diagnostic and prognostic applications necessitates a near perfect data generation. To assess the usability of a widely used HTS platform for accurate and reproducible clinical applications in terms of robustness, we generated whole genome shotgun (WGS) sequence data from the genomes of two human individuals in two different genome sequencing centers. After analyzing the data to characterize SNPs and indels using the same tools (BWA, SAMtools, and GATK), we observed significant number of discrepancies in the call sets. As expected, the most of the disagreements between the call sets were found within genomic regions containing common repeats and segmental duplications, albeit only a small fraction of the discordant variants were within the exons and other functionally relevant regions such as promoters. We conclude that although HTS platforms are sufficiently powerful for providing data for first-pass clinical tests, the variant predictions still need to be confirmed using orthogonal methods before using in clinical applications.

Document type: 
Article
File(s): 

Rethinking Colour Constancy

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2015
Abstract: 

Colour constancy needs to be reconsidered in light of the limits imposed by metamer mismatching. Metamer mismatching refers to the fact that two objects reflecting metameric light under one illumination may reflect non-metameric light under a second; so two objects appearing as having the same colour under one illuminant can appear as having different colours under a second. Yet since Helmholtz, object colour has generally been believed to remain relatively constant. The deviations from colour constancy registered in experiments are usually thought to be small enough that they do not contradict the notion of colour constancy. However, it is important to determine how the deviations from colour constancy relate to the limits metamer mismatching imposes on constancy. Hence, we calculated metamer mismatching’s effect for the 20 Munsell papers and 8 pairs of illuminants employed in the colour constancy study by Logvinenko and Tokunaga and found it to be so extensive that the two notions—metamer mismatching and colour constancy—must be mutually exclusive. In particular, the notion of colour constancy leads to some paradoxical phenomena such as the possibility of 20 objects having the same colour under chromatic light dispersing into a hue circle of colours under neutral light. Thus, colour constancy refers to a phenomenon, which because of metamer mismatching, simply cannot exist. Moreover, it obscures the really important visual phenomenon; namely, the alteration of object colours induced by illumination change. We show that colour is not an independent, intrinsic attribute of an object, but rather an attribute of an object/light pair, and then define a concept of material colour in terms of equivalence classes of such object/light pairs. We suggest that studying the shift in material colour under a change in illuminant will be more fruitful than pursuing colour constancy’s false premise that colour is an intrinsic attribute of an object.

Document type: 
Article
File(s): 

Genome-wide variations in a natural isolate of the nematode Caenorhabditis elegans

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2014
Abstract: 

Background

Increasing genetic and phenotypic differences found among natural isolates of C. elegans have encouraged researchers to explore the natural variation of this nematode species.

Results

Here we report on the identification of genomic differences between the reference strain N2 and the Hawaiian strain CB4856, one of the most genetically distant strains from N2. To identify both small- and large-scale genomic variations (GVs), we have sequenced the CB4856 genome using both Roche 454 (~400 bps single reads) and Illumina GA DNA sequencing methods (101 bps paired-end reads). Compared to previously described variants (available in WormBase), our effort uncovered twice as many single nucleotide variants (SNVs) and increased the number of small InDels almost 20-fold. Moreover, we identified and validated large insertions, most of which range from 150 bps to 1.2 kb in length in the CB4856 strain. Identified GVs had a widespread impact on protein-coding sequences, including 585 single-copy genes that have associated severe phenotypes of reduced viability in RNAi and genetics studies. Sixty of these genes are homologs of human genes associated with diseases. Furthermore, our work confirms previously identified GVs associated with differences in behavioural and biological traits between the N2 and CB4856 strains.

Conclusions

The identified GVs provide a rich resource for future studies that aim to explain the genetic basis for other trait differences between the N2 and CB4856 strains.

Document type: 
Article
File(s): 

Ribofsm: Frequent Subgraph Mining For the Discovery of RNA Structures and Interactions

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2014
Abstract: 

Frequent subgraph mining is a useful method for extracting meaningful patterns from a set of graphs or a single large graph. Here, the graph represents all possible RNA structures and interactions. Patterns that are significantly more frequent in this graph over a random graph are extracted. We hypothesize that these patterns are most likely to represent biological mechanisms. The graph representation used is a directed dual graph, extended to handle intermolecular interactions. The graph is sampled for subgraphs, which are labeled using a canonical labeling method and counted. The resulting patterns are compared to those created from a randomized dataset and scored. The algorithm was applied to the mitochondrial genome of the kinetoplastid species Trypanosoma brucei, which has a unique RNA editing mechanism. The most significant patterns contain two stem-loops, indicative of gRNA, and represent interactions of these structures with target mRNA.

Document type: 
Article
File(s):