Find research datasets worth reusing

opencc-by-4.0Dec 2005View details →

Fig. 4. Hemiancistrus subviridis MCNG 54032, 133.5 in Baryancistrus demantoides and Hemiancistrus subviridis, two new uniquely colored species of catfishes from Venezuela (Siluriformes: Loricariidae)

Fig. 4. Hemiancistrus subviridis MCNG 54032, 133.5 mm SL; holotype, dorsal, lateral, and ventral views. Photos by D.C. Werneke.

opencc-by-4.0Dec 2005View details →

Fig. 2. Baryancistrus demantoides MCNG 54029, 150.5 in Baryancistrus demantoides and Hemiancistrus subviridis, two new uniquely colored species of catfishes from Venezuela (Siluriformes: Loricariidae)

Fig. 2. Baryancistrus demantoides MCNG 54029, 150.5 mm SL; holotype, dorsal, lateral, and ventral views. Photos by D.C. Werneke.

opencc-by-4.0Dec 2005View details →

Fig. 1 in Baryancistrus demantoides and Hemiancistrus subviridis, two new uniquely colored species of catfishes from Venezuela (Siluriformes: Loricariidae)

Fig. 1. Live specimens of a: Baryancistrus demantoides, adult, AUM 42034, paratype, 96.3 mm SL; b: B. demantoides, juvenile, MCNG 54031, paratype, 54.1 mm SL; c: Hemiancistrus subviridis, AUM 42933, 146.9 mm SL. Photos by M.H. Sabaj.

opencc-zeroOct 2022View details →

Haemosporidian parasites and incubation period influence plumage coloration in tanagers (Passeriformes: Thraupidae)

Birds are visually oriented and use their plumage coloration as an important signaling trait in social communication. Males and females may have different patterns of plumage coloration, a phenomenon known as sexual dichromatism. Because males tend to have more complex plumages, sexual dichromatism is usually attributed to female choice. However, plumage coloration is partly condition-dependent, therefore other selective pressures affecting individuals' success may also drive the evolution of this trait. Here we used tanagers to study the relationships between dichromatism and plumage coloration complexity with parasitism by haemosporidians, investment in reproduction, and life-history traits. We screened blood samples from 2849 birds belonging to 52 tanager species for detecting haemosporidian parasites. We used publicly available data for plumage coloration, bird phylogeny, and life-history traits to run models with plumage dichromatism and complexity in males and females. We found that dichromatism was more pronounced in bird species with higher prevalence of haemosporidian parasites. Lastly, females with high plumage coloration complexity were associated with a longer incubation period. Our results indicate an association between haemosporidian parasites and plumage coloration suggesting that parasites impact mechanisms of both sexual selections, increasing differences between sexes, and social (non-sexual) selection, driving females to develop more complex colorations.

opencc-by-4.0Dec 2022View details →

Data used in "The Utility of RGB Color for Discrimination of Lunar Maturity and Composition"

Datasets from the paper "The Utility of RGB Color for Discrimination of Lunar Maturity and Composition", By D. T. Blewett, T. X. Choi, Y.-C. Zheng, and E. A. Cloutis, to be published in the journal Earth and Space Science. Reflectance spectra for Apollo lunar samples 14003, 15601, 70011, 14310, and 65015 were published by Wagner et al. (1987), Icarus 69, 14–28. The spectra were digitized by Amanda Hendrix and Faith Vilas (see Hendrix and Vilas (2006), Astron. J. 132, 1396–1404). I took the spectra that Hendrix and Vilas supplied to me and resampled them to RELAB wavelengths. The spectra are in a tab-delimited text file. The responsivities of the Chang'E-3 PCAM RGB channels were published by X. Ren et al. (2014), Res. Astron. Astrophys. 14, 1557–1566. We digitized the RGB curves from Fig. 2 of the Ren paper. The curves are in tab-delimited text files.

opencc-zeroDec 2022View details →

Representations of color and form in mouse visual cortex

Spatial transitions in color can aid any visual perception task, and its neural representation – an "integration of color and form" – is thought to begin at primary visual cortex (V1). Color and form integration is untested in mouse V1, yet studies show that the ventral retina provides the necessary substrate from green-sensitive rods and UV-sensitive cones. Here, we used two-photon imaging in V1 to measure spatial frequency (SF) tuning along four axes of rod and cone contrast space, including luminance and color. We first reveal that V1 has similar responsiveness to luminance and color, yet average SF tuning is significantly shifted lowpass for color. Next, guided by linear models, we used SF tuning along all four color axes to estimate the proportion of neurons that fall into classic models of color opponency – "single-", "double-", and "non-opponent". Few neurons (~6%) fit the criteria for double-opponency, which are uniquely tuned for chromatic borders. Most of the population can be described as a unimodal distribution ranging from strongly single-opponent to non-opponent. Consistent with recent studies of the rodent and primate retina, our V1 data is well-described by a simple model in which ON and OFF channels to V1 sample the photoreceptor mosaic randomly.

opencc-zeroJul 2019View details →

IODP Expedition 376 Color reflectance

Color reflectance data were measured on section halves using an integration sphere and a UV-VIS spectrophotometer mounted on the Section Half Multisensor Logger (SHMSL). Spectral counts are recorded in the range of 380 to 700 nm, covering the visible spectrum, and binned in ~2 nm bins. Spectral data are reduced from spectra and recorded in tristimulus XYZ values, CieLAB L*a*b* values, and other units.

2 million histopathology stain vectors including Hematoxylin & Eosin color variations

The database includes the stain vectors including color variations of over 2 million patches. The database is adopted in "Data-driven color augmentation for H&E stained images in computational pathology", (https://www.sciencedirect.com/science/article/pii/S2153353922007830) to check is the color variation of an augmentated sample is acceptable or not. During the training, the color variation of an augmented sample is compared with the variations included in the database. If N variations from the database are found within a radius R from the components of the augmented sample, the augmented sample is considered acceptable (in terms of color variations); otherwise, it is discarded. The database is stored in a .pickle file, including vectors with six elements: the RGB components of Hematoxylin and Eosin, for every patch. Double entries are removed from the database. Code to import and to extend database with new data is available here: https://github.com/ilmaro8/Data_Driven_Color_Augmentation Stain vectors are collected from six private and public sources, to ensure that color variations can cover the variability of H&E-stained tissues: TCGA, ExaMode colon dataset, Camelyon, Puerta del Mar, Clinic, CAD.

Dataset: Invariant categorical color regions across illuminant change coincide with focal colors

Experimental data for a paper titled "Invariant categorical color regions across illuminant change coincide with focal colors“ published in Journal of Vision. This repository contains following data. Please refer to the article for details about the dataset.   1. IlluminantsANDReflectances.xlsx This file stores spectral radiance for each illuminant and OSA coordinates (jgL) and reflectance values for 424 OSA color samples.   2. Exp1_1_RawData Raw data for Experiment 1-1. This folder has xlsx files, and filename indicates the illuminant condiion. In each xlsx file, different sheets contain a different observer’s data. The number (1-424) corresponds to the number of OSA sample (shown in IlluminantsANDReflectances.xlsx).   3. Exp1_2_RawData Raw data for Experiment 1-2. The same format as Exp1_1_RawData.   4. Exp2_RawData.xlsx Raw matching data for Experiment 2. The name of each sheet shows the observer & illuminant condition. Each row shows Ljg coordinates of the OSA sample and associated matching result (in RGB and xyL).

opencc-by-4.0Dec 2022View details →

Text-fig. 1. The Catefica exposure along the road between Catefica and Mugideira photographed in 1989 when the mesofossil flora was discovered. The exposed strata are mainly cross-bedded light colored sands, darker horizons of clay and dark lenses with mesofossils. The most productive sample, Catefica sample 49, was collected in the basal part of the exposed sequence (arrow head). One of the authors (PRC) exploring the middle part of the section. Photo K. R. Pedersen. in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms

Text-fig. 1. The Catefica exposure along the road between Catefica and Mugideira photographed in 1989 when the mesofossil flora was discovered. The exposed strata are mainly cross-bedded light colored sands, darker horizons of clay and dark lenses with mesofossils. The most productive sample, Catefica sample 49, was collected in the basal part of the exposed sequence (arrow head). One of the authors (PRC) exploring the middle part of the section. Photo K. R. Pedersen.

Dataset: Modelling surface color discrimination under different lighting environments using image chromatic statistics and convolutional neural networks

Associated publication [1] Samuel Ponting*, Takuma Morimoto*, Hannah E. Smithson, “Modelling surface color discrimination under different lighting environments using image chromatic statistics and convolutional neural networks”, *equal contribution, bioRxiv, <a href="https://www.google.com/url?q=https%3A%2F%2Fdoi.org%2F10.1101%2F2022.11.02.514864&sa=D&sntz=1&usg=AOvVaw3KwSo7KmqPzBR1UMc1MHmk">https://doi.org/10.1101/2022.11.02.514864</a> [2] Takuma Morimoto, and Hannah E. Smithson, “Discrimination of spectral reflectance under complex environmental illumination,” Journal of the Optical Society of America A, 35, 4, B244-B255 (2018) https://doi.org/10.1364/JOSAA.35.00B244   Datasets contain 2 folders and 1 mat file.   (Folder 1) Stimuli (Folder 2) Psychophysics_data (Mat file) stimulusMagnitudeToMacLeodBoynton.mat   Details are described below.   ---------------------------------------------------------------------------------------------------------------------------------------- (Folder 1) Stimuli   Overview of datasets This Image dataset includes 57,600 images (2 gloss levels * 3 environments * 100 stimulus magnitudes * 8 hue directions * 12 camera angles from 0 to 330 degree in 30 degree step) in .mat format.   The half of images were used in psychophysical experiment (camera angles: 0, 60, 120, 180, 240, 300 degrees). Other half images were used for testing chromatic statistics models and CNN-based models [1] (camera angles: 30, 90, 150, 210, 270, 330 degrees).   Each image file Filename denotes a condition name and the camera angle as formatted in a following way.   stim_”environment” _”glossiness”_”hueAngle”_”magnitude”_”cameraAngle”.mat e.g. “stim_en1_glossy_hue45_n45_cameraAngle90.mat”   Stimulus magnitude 100 is a maximum saturation, and 1 corresponds to equal energy white (which was used as a distractor object).   Each image file contains two valuables : MacLeodBoynton, XYZ   Each variable contains an image of 128*128*3 pixels (height*width*channel).   MacLeod-Boynton: MacLeod-Boynton chromaticity image (1st channel: L/(L+M), 2nd channel: S/(L+M), and 3rd channel L+M) XYZ: XYZ coordinates calculated based on 2-degree CIE 1931 xyz color matching function (1st channel: X, 2nd channel: Y, and 3rd channel Z)   Luminance and L+M are both relative (normalised by the maximum luminance across all 57,600 images).   ---------------------------------------------------------------------------------------------------------------------------------------- (Folder 2) Psychophysics_data Filename denotes the condition and observers formatted in a following way.   data_”environment” _”specularities”_”sessionNumber”_”obsever”.mat e.g. data_en2_matte_session4_JH.mat or .csv   Each file includes following variables:   (Variable 1) threshold Thresholds are stored in MacLeod-Boynton (MB) chromaticity coordinates for all 8 hue directions (from 0 to 315 degree in 45 degree step).   MacLeod-Boynton chromaticity coordinates were calculated in a following way. These scalings are in accordance with description in CVRL main site (Chromaticity coordinates tab ).   First of all, L, M, and S cone signals were calculated based on Stockman & Sharpe cone fundamentals (energy in linear scale available at at http://www.cvrl.org). Each sensitivity curve was normalised to have 1.0 at the peak.   Then, MB coordinates were calculated using equation (1-3).   L/(L+M) = Lw*L/(Lw*L+Mw*M) - (1) S/(L+M) = Sw*S/(Lw*L+Mw*M) - (2) L+M = Lw*L+Mw*M - (3)   where Lw = 0.689903; Mw = 0.348322;Sw = 1.93540.   L, M and S denote L-cone, M-cone, S-cone excitations, respectively.   Under this calculation, equal energy white becomes L/(L+M) = 0.7078 and S/(L+M) = 1.   (Variable 2) staircase   Since we ran 8 interleaved staircase (for 8 hue angles), information about 8 staircases are stored in this single variable. (staircase(1) corresponds to 0 degree, and staircase(8) corresponds to 315 degree)   There are 5 fields: (i) groundtruth, (ii) response, (iii) correct, (iv) magnitude, (v) cameraAngle   For each trial, the location of objects was defined in a following way. | 1 3 | | 2 4 |   And each field stores following information for all trials in the staircase.   (i) groundtruth Location of the target object   (ii) response Location that the participant chose   (iii) correct If the response was correct (1) or incorrect (0)   (iv) magnitude Stimulus magnitude of target object in each trial from 1 to 100 (1 for equal energy white and 100 for maximum saturation).   (v) Camera angle Camera angles assigned for four objects in each trial. This data and (i) groundtruth allow reconstruct of the exact image for each trial.   ---------------------------------------------------------------------------------------------------------------------------------------- (Mat file) stimulusMagnitudeToMacLeodBoynton.mat This file stores a variable ‘stimulusMagnitudeToMacLeodBoynton’ (8*100*2) which describes correspondence map between stimulus magnitude and MacLeod-Boynton chromaticity.   1st channel: hue direction from 0 degree to 315 degree, 45 degree step 2nd channel: magnitude from 1 to 100 3rd channel: MacLeod-Boynton coordinate, 1 being L/(L+M) and 2 being S/(L+M)

opencc-zeroJan 2023View details →

Ultraviolet vision in anemonefish improves color discrimination

In many animals, ultraviolet (UV) vision guides navigation, foraging, and communication, but few studies have addressed the contribution of UV vision to color discrimination, or behaviorally assessed UV discrimination thresholds. Here, we tested UV-color vision in an anemonefish (Amphiprion ocellaris) using a novel five-channel (RGB-V-UV) LED display designed to test UV perception. We first determined that the maximal sensitivity of the A. ocellaris UV cone was at ~386 nm using microspectrophotometry. Three additional cone spectral sensitivities had maxima at ~497, 515, and ~535 nm, which together informed the modelling of the fish's color vision. Anemonefish behavioral discrimination thresholds for nine sets of colors were determined from their ability to distinguish a colored target pixel from grey distractor pixels of varying intensity. We found that A. ocellaris used all four cones to process color information and is therefore tetrachromatic, and fish were better at discriminating colors (i.e., color discrimination thresholds were lower, or more acute) when targets had UV chromatic contrast elicited by greater stimulation of the UV cone relative to other cone types. These findings imply that a UV component of color signals and cues improves their detectability, which likely increases the salience of anemonefish body patterns used in communication and the silhouette of zooplankton prey.

Chromosome-scale genome assembly and insights into the metabolome and gene regulation of leaf color transition in an important oak species, Quercus dentata

Quercus dentata Thunb., a dominant forest tree species in northern China, has significant ecological and ornamental value due to its adaptability and beautiful autumn coloration, with color changes from green to yellow into red resulting from the autumnal shifts in leaf pigmentation. However, the key genes and molecular regulatory mechanisms for leaf color transition remain to be investigated. First, we presented a high-quality chromosome-scale assembly for Q. dentata. This 893.54 Mb sized genome (contig N50=4.21 Mb, scaffold N50=75.55 Mb; 2n=24) harbors 31,584 protein-coding genes. Second, our metabolome analyses uncovered pelargonidin-3-O-glucoside, cyanidin-3-O-arabinoside, and cyanidin-3-O-glucoside as the main pigments involved in leaf color transition. Third, gene co-expression further identified the MYB-bHLH-WD40 (MBW) transcription activation complex as central to anthocyanin biosynthesis regulation. Notably, transcription factor (TF) QdNAC (QD08G038820) was highly co-expressed with this MBW complex and may regulate anthocyanin accumulation and chlorophyll degradation during leaf senescence through direct interaction with another TF, QdMYB (QD01G020890), as revealed by our further protein-protein and DNA-protein interaction assays. Our high-quality genome assembly, metabolome and transcriptome resources further enrich Quercus genomics, and will facilitate upcoming exploration of ornamental values and environmental adaptability in this important genus.

opencc-zeroJan 2023View details →

Interspecific hybridization explains rapid gorget color divergence in Heliodoxa hummingbirds (Aves: Trochilidae)

Hybridization is a known source of morphological, functional, and communicative signal novelty in many organisms. Although diverse mechanisms of established novel ornamentation have been identified in natural populations, we lack an understanding of hybridization effects across levels of biological scales and upon phylogenies. Hummingbirds display diverse structural colors resulting from coherent light scattering by feather nanostructures. Given the complex relationship between feather nanostructures and the colors they produce, intermediate coloration does not necessarily imply intermediate nanostructures. Here, we characterize nanostructural, ecological, and genetic inputs in a distinctive Heliodoxa hummingbird from the foothills of eastern Peru. Genetically, this individual is closely allied with Heliodoxa branickii and H. gularis, but it is not identical to either when nuclear data are assessed. Elevated interspecific heterozygosity further suggests it is a hybrid backcross to H. branickii. Electron microscopy and spectrophotometry of this unique individual reveal key nanostructural differences underlying its distinct gorget color, confirmed by optical modeling. Phylogenetic comparative analysis suggests that the observed gorget coloration divergence from both parentals to this individual would take 6.6–10 My to evolve at the current rate within a single hummingbird lineage. These results emphasize the mosaic nature of hybridization and suggest that hybridization may contribute to the structural color diversity found across hummingbirds.

opencc-by-4.0Feb 2023View details →

NIR-MFCO dataset: Near-infrared-based false-color images of post-consumer plastics at different material flow compositions and material flow presentations

Determining mass-based material flow compositions (MFCOs) is crucial for assessing and optimizing the recycling of post-consumer plastics. Currently, MFCOs in plastic recycling are mostly determined through manual sorting analysis, but the use of inline near-infrared (NIR) sensors holds potential to automate the characterization process, paving the way for novel sensor-based material flow characterization (SBMC) applications. The NIR-MFCO dataset aims to expedite SBMC research by providing NIR-based false-color images of plastic material flows with their corresponding MFCOs. The false-color images were created through the pixel-based classification of binary material mixtures using a hyperspectral imaging camera (EVK HELIOS NIR G2-320; 990 nm – 1678 nm wavelength range) and the on-chip classification algorithm (CLASS 32). The resulting NIR-MFCO dataset includes n = 880 false-color images from three test series: (T1) high-density polyethylene (HDPE) and polyethylene terephthalate (PET) flakes, (T2a) post-consumer HDPE packaging and PET bottles, and (T2b) post-consumer HDPE packaging and beverage cartons for n = 11 different HDPE shares (0% - 50%) at four different material flow presentations (singled, monolayer, bulk height H1, bulk height H2). The dataset can be used, e.g., to train machine learning algorithms, evaluate the accuracy of inline SBMC applications, and deepen the understanding of segregation effects of anthropogenic material flows, thus further advancing SBMC research and enhancing post-consumer plastic recycling.

opencc-zeroFeb 2023View details →

Evolutionary insights into Felidae iris color through ancestral state reconstruction

There have been almost no studies with an evolutionary perspective on eye (iris) color, outside of humans and domesticated animals. Extant members of the family Felidae have a great interspecific and intraspecific diversity of eye colors, in stark contrast to their closest relatives, all of which have only brown eyes. This makes the felids a great model to investigate the evolution of eye color in natural populations. Through machine learning cluster image analysis of publicly available photographs of all felid species, as well as a number of subspecies, five felid eye colors were identified: brown, hazel/green, yellow/beige, gray, and blue. Using phylogenetic comparative methods, the presence or absence of these colors was reconstructed on a phylogeny. Additionally, through a new color analysis method, the specific shades of the ancestors' eyes were quantitatively reconstructed. The ancestral felid population was predicted to have brown-eyed individuals, as well as a novel evolution of gray-eyed individuals, the latter being a key innovation that allowed the rapid diversification of eye color seen in modern felids, including numerous gains and losses of different eye colors. It was also found that the loss of brown eyes and the gain of yellow/beige eyes is associated with an increase in the likelihood of evolving round pupils, which in turn influence the shades present in the eyes. Along with these important insights, the unique methods presented in this work are widely applicable and will facilitate future research into phylogenetic reconstruction of color beyond irises.

opencc-zeroFeb 2023View details →

Data from: Disruptive selection and the evolution of discrete color morphs in Timema stick insects

A major unresolved issue in biology is why phenotypic and genetic variation is sometimes continuous, yet other times packaged into discrete units of diversity, such as morphs, ecotypes, and species. In theory, ecological discontinuities can impose strong disruptive selection that promotes the evolution of discrete forms, but direct tests of this hypothesis are lacking. Here we show that Timema stick insects exhibit genetically-determined color morphs that range from weakly to strongly discontinuous. Color data from nature and a manipulative field experiment demonstrate that greater morph differentiation is associated with shifts from host plants exhibiting more continuous color variation to those exhibiting greater coloration distance between green leaves and brown stems, the latter of which generates strong disruptive selection. Our results show how ecological factors can promote discrete variation, and we further present results on how this can have variable effects on the genetic differentiation that promotes speciation.

opencc-by-4.0Apr 2023View details →

A 5 m multi-scale topographic position color composite (MTPCC) across France

The multi-scale topographic position color composite (MTPCC) describes the position of a pixel relative to its neighborhood at several spatial scales. It was derived from the national airborne DTM (RGE ALTI ®) at 5 m spatial resolution, which is available from the website of the French National Geographic Institute (IGN) (<a href="https://geoservices.ign.fr/">https://geoservices.ign.fr/</a>). Dataset includes: <ul> <li>280 GeoTIFF raster files (MTPCC_000.tif) projected in the French Lambert-93 system (EPSG code 2154), each file corresponding to a 50 x 50 km tile. The number indicates the tile of interest ;</li> <li>1 vector tile index at Google Earth format (tile_index.kmz) showing the location of each tile. This file has been created to facilitate download layer only on area of interest.</li> </ul> To reduce storage space and download time, each raster file has been packed at 7-Zip freeware format. A complete description of the dataset can be found in Panhelleux, L., Rapinel, S., Lemercier, B., Gayet, G., Hubert-Moy, L., 2023. A 5 m dataset of digital terrain model derivatives across mainland France. Data in Brief 109369. https://doi.org/10.1016/j.dib.2023.109369

opencc-zeroApr 2023View details →

Complex plumages spur rapid color diversification in kingfishers (Aves: Alcedinidae)

Colorful signals in nature provide some of the most stunning examples of rapid phenotypic evolution. Yet, studying color pattern evolution has been historically difficult owing to differences in perceptual ability of humans and analytical challenges with studying how complex color patterns evolve. Island systems can provide a natural laboratory for testing hypotheses about the direction and magnitude (i.e., rate) of phenotypic change. A recent study of bird coloration found that the plumages of island species are darker and less complex than continental species. Whether such shifts in plumage complexity are associated with increased rates of color evolution on islands remains unknown. Here, we use geometric morphometric techniques to test the hypothesis that plumage complexity and island insularity interact to influence color diversity in a species-rich and cosmopolitan clade of colorful birds—kingfishers (Aves: Alcedinidae). In particular, we test three predictions: i) plumage complexity enhances interspecific rates of color evolution, ii) plumage complexity is lower on islands, and iii) rates of plumage color evolution are higher within island systems. Our results show that more complex plumages result in more diverse colors among species and that island species have higher rates of color evolution. Importantly, we found that island species did not have more complex plumages than their continental relatives. Thus, complexity may be a key innovation that facilitates response to relaxed (or divergent) selection pressures on islands. Lack of strong support for competition-driving rates of evolution along different color axes hints at an allopatric model of color evolution in which species adapt to local conditions on different islands. This study demonstrates how a truly multivariate treatment of color data can reveal evolutionary patterns that might otherwise go unnoticed.