Find research datasets worth reusing

opencc-by-4.0Jun 2024View details →

Combining reference-star and angular differential imaging for high-contrast imaging of extended sources - Appendix

This appendix presents the disk estimations obtained with RDI, ADI, and ARDI, using IPCA, for all 60 test data sets considered in Juillard et. al. (2024). Page-sized figures shows IPCA disk estimations obtained leveraging RDI, ADI and ARDI strategies for cube 1 to 4 and disks A to E. Details on the data sets where disks were injected can be found in Juillard et. al. (2023) and Juillard et. al. (2024), and can be found on the Zeneodo folder : <a href="../records/11442267">https://zenodo.org/records/11442267</a> Each page-sized figure presents the results for a specific synthetic disk in a given data set. The injected disks (A→E) are shown in the left-most column of each figure. Each figure contains three pairs of rows, each corresponding to a different injected contrast level: $10^{-3}$ (top), $10^{-4}$ (middle), and $10^{-5}$ (bottom). The top row of each pair represents the estimation, while the bottom row represents the residuals. Each column displays the following in order: ground truth (left), RDI (middle left), ADI (middle right), and ARDI (right). The best method, as determined by each metric, is indicated in the bottom-left corner of each pair of rows. The color bar bounds in the residual plots is set to $\pm$ maximum of intensity of the GT, centered at 0. For the disk image estimation plots, the color bar is adjusted for each data set to have a maximum value equal to the 99th percentile of the image. The minimal value is set to 0. Additionally, the optimal IPCA parameters (rank and number of iterations) are written at the top left of the corresponding images.

opencc-by-4.0Dec 2023View details →

Figure 1 in Genetic difference between two Schistosoma japonicum isolates with contrasting cercarial shedding patterns revealed by whole genome sequencing

Figure 1. Map of geographical locations of research sites.

Data pertaining to the published article "Detection of pathological contrast enhancement with synthetic brain imaging from quantitative multiparametric MRI" by Donatelli et al., 2024

Data pertaining to the published article "Detection of pathological contrast enhancement with synthetic brain imaging from quantitative multiparametric MRI" by Donatelli et al., 2024. <a href="https://doi.org/10.1111/jon.13201">https://doi.org/10.1111/jon.13201</a>

Contrast in Sprite and Elve productions from a coastal thunderstorm in eastern Spain [Dataset]

<a name="_Hlk172282785"></a>Data for the study on the production conditions of 58 sprites and 14 elves observed during a storm over the eastern Mediterranean coast of Spain during the night of November 27 to 28, 2016: optical data from two sensitive cameras, characteristics of the lightning activity and cloud top temperature from the radiometer onboard the Meteosat Second Generation satellite reveal striking contrasts regarding the two types of phenomena.

Dataset for Modelling of infiltration rates in soils derived from contrasting parent materials using Horton's model

This dataset was initially generated as part of a broader project investigating infiltration and various soil properties in soils derived from three parent materials in Akwa Ibom State, Nigeria: Alluvial Clay, Coastal Plain Sands, and Sandstone. Utin and Oguike (2018) initially utilized this data to evaluate Philip's and Kostiakov's models in these soils. Subsequently, the infiltration data were employed as secondary data to assess the performance of Horton's model in predicting infiltration rates for the three soil types.

opencc-by-sa-4.0Jul 2024View details →

Differential interference contrast (DIC) image of unstained living HepG2 human liver cancer cells

Introduction This dataset is associated with our submission to Computers in Biology and Medicine, titled "Accurate Detection and Instance Segmentation of Unstained Living Adherent Cells in Differential Interference Contrast Images". The submission number for this manuscript is CIBM-D-23-09623R1. Authors: Fei Pan, Yutong Wu, Kangning Cui, Shuxun Chen, Yanfang Li, Yaofang Liu, Adnan Shakoor, Han Zhao, Beijia Lu, Shaohua Zhi, Raymond Hon-Fu Chan, Dong Sun Dataset Description Our dataset comprises 520 differential interference contrast (DIC) images of 12,198 unstained HepG2 human liver cancer cells, each with a corresponding fluorescence image stained with calcein acetoxymethyl (AM), ensuring high-quality ground-truth annotations. Unique in addressing the multi-state nature of adherent cells commonly seen in wet labs, it includes both healthy and unhealthy cells in a single image, providing a valuable resource for studying multi-state cell detection and instance segmentation. Citation We kindly request that researchers who use this dataset cite both our paper and this dataset. This will help acknowledge the work and facilitate further advancements in the field. Please cite as follows: Paper: Pan, F., Wu, Y., Cui, K., Chen, S., Li, Y., Liu, Y., Shakoor, A., Zhao, H., Lu, B., Zhi, S., Chan, R. H.-F., & Sun, D. "Accurate detection and instance segmentation of unstained living adherent cells in differential interference contrast images,” Computers in Biology and Medicine, vol. 182, p. 109151, Nov. 2024, doi: 10/g5p9d8. Dataset: Pan, F., Chen, S., Li, Y., Shakoor, A., Zhao, H., & Sun, D. (2024). Differential interference contrast (DIC) image of unstained living HepG2 human liver cancer cells. Zenodo.  Thank you for your interest and support in our work. We look forward to seeing the innovative research that this dataset will enable.

opencc-by-4.0Jun 2018View details →

Space rocks and optimising scanning electron channelling contrast Dataset

Data bundle for "Space rocks and optimising scanning electron channelling contrast" Ben Britton, Daniel Goran, Vivian Tong Accepted for publication in Materials Characterization https://doi.org/10.1016/j.matchar.2018.06.001 Also available as an ArXiv preprint: https://arxiv.org/abs/1804.08754 Contact Dr Ben Britton - e: b.bbritton@imperial.ac.uk; t: @bmatb Contents: Figures - high resolution images of the figures that were included in the paper. Rot_series - the full rotation series, including the rotation stacked as a gif. DD_series - the full detector retraction series, including these stacked as a gif. DTilt_series - the full detector retraction series, including these stacked as a gif. Raw_Images - is a full folder of the images with cropped and full ROI (which stack) for each of the images, including the results from the EBSP fits. To request the EBSD data, please contact Dr Britton directly.

opencc-by-4.0Sep 2018View details →

Response of E3 stage Radix balthica embryos maintained in contrasting temperatures and salinities for 24h

Sample datasets and video acquired using the EmbryoPhenomics platform. Experiment assessing influence of three (20, 25 and 30C) contrasting temperatures and two salinities (0 or 7 ppt) on the development of the aquatic gastropod Radix balthica. Exposure was initiated at the E3 developmental stage at which embryos are undergoing ciliary driven spinning. The EmbryoCV package was used to produce phenome-level data. Datasets and associated video for an individual embryo from each treatment (temperature and salinity combinations).

opencc-by-4.0Sep 2018View details →

Development of Radix balthica embryos under contrasting temperatures for the duration of their development

Sample datasets, HR modelling data and video acquired using the EmbryoPhenomics platform. Experiment assessing influence of three (20, 25 and 30C) contrasting temperatures on the development of the aquatic gastropod Radix balthica. Imaging was performed from first cell division to hatching and the EmbryoCV package was used to produce phenome-level data. Datasets and associated video for an individual embryo from each temperature are provided. EmbryoPhenomics datasets can be accessed using the XArray library in Python (or if EmbryoCV is installed see www.embryocv.org for instructions on loading data): <ul> <li>results = xr.open_mfdataset(path_to_file). This will reveal the various data arrays.</li> </ul> EmbryoPhenomics HR data can be loaded using the Numpy library in Python: <ul> <li>hr = np.load(path_to_file)[()] filt = hr[embryoLabel i.e. B3, C5 or D6] </li> </ul>

opencc-by-4.0Jan 2019View details →

Phase contrast microscopy sequence of U373 cells.

The .zip file contains .CSV file for frame each line contains: #cell, #frame, x position, y position Cell cultures in Falcon plastic dishes maintained at 37 C° were observed and recorded automatically every 4 min. The images were acquired under a phase-contrast microscope (Olympus, model IX50, magnification ratio 10:1), with a charge-coupled device video camera (Hitachi Denshi, modelKP-M1E/K-S10) coupled with an acquisition board (32-bits Matrix Vision PC-GRAB-GI frame grabber). The image dimensions are 700 500 pixels (with a pixel resolution of 0.92µm at the magnification ratio abovementioned) discretized on 256 gray levels (8 bits/pixel). The images are compressed using jpeg compression.

Sample files for auto_SAR_Ocean_Contrast (autonomous Ocean Contrast Estimation for SAR Images)

Sample input and output files for the open source code auto_SAR_Ocean_Contrast (autonomous Ocean Contrast Estimation for SAR Images). auto_SAR_Ocean_Contrast is a python module for estimating the contrast in a SAR image of the ocean surface, relative to clean water pixels. The code is primarily intended to identify oil slicks, but can be used to identify any radar-dark feature in a scene that is not entirely radar-dark. The contrast ratio is often referred to as the damping ratio in the scientific literature concerning mineral oil slicks. github repository:

opencc-by-4.0Aug 2023View details →

Contrasting Views of the Electric Double Layer in Electrochemical CO2 Reduction: Continuum Models vs Molecular Dynamics (data for figures)

This is the data used to create the figures in the article: <h4>Contrasting Views of the Electric Double Layer in Electrochemical CO2 Reduction: Continuum Models vs Molecular Dynamics</h4> <div>Evan Johnson and Sophia Haussener</div> <div>The Journal of Physical Chemistry C 2024 128 (25), 10450-10464</div> DOI: 10.1021/acs.jpcc.4c03469 See the file "Naming conventions" for the file names and column/row meanings.

opencc-by-4.0Aug 2024View details →

Neural pathways and computations that achieve stable contrast processing tuned to natural scenes

<h1>Gur et al. 2024 database</h1> Source data of the paper Gür et al. 2024, “Neural pathways and computations that achieve stable contrast processing tuned to natural scenes”, Nature Communications. This work contains an analysis of post-receptor luminance gain in the Drosophila visual system, focusing on the circuitry and algorithms for implementation of rapid luminance gain control. All data can be analyzed using the code provided in the Github repository: <a href="https://github.com/silieslab/Gur-etal-2024">https://github.com/silieslab/Gur-etal-2024</a>. Please go to the “Readme” file in the repository for how to use the code. <h2>Raw data</h2> All raw data is located in the folder “raw_data”. "Readme" file located in the code repository will guide you on how to analyze all data. <h2>Processed data</h2> All processed data is located in the folder “processed_data”. "Readme" file located in the code repository will guide you on how to analyze all data. - 2p_imaging_python_pickle: Processed data stored as .pickle files.  - Dm12_Figure7_Mat_files: Processed data for Dm12 imaging and optogenetics experiments presented in Figure 7 stored as .mat files. - EM_data: Processed data for EM analysis done in Figure 7. - Figure 6 Tm9 flpSTOP: tdTomato expression data for Figure 6 Tm9 flpSTOP experiments. - Figure S5 Tm1 flpSTOP: tdTomato expression data for FigureS5 Tm1 flpSTOP experiments.

opencc-by-4.0May 2024View details →

Data and code for "Contrasting Chlorine Chemistry on Volcanic and Wildfire Aerosols in the Southern Mid-Latitude Lower Stratosphere"

Data and code for the paper entitled "Contrasting Chlorine Chemistry on Volcanic and Wildfire Aerosols in the Southern Mid-Latitude Lower Stratosphere"

opencc-by-4.0Oct 2024View details →

Supplementary data to: Characterizing regional oceanography and bottom environmental conditions at two contrasting sponge grounds on the northern Labrador Shelf.

Supplementary data to the article:  Characterizing regional oceanography and bottom environmental conditions at two contrasting sponge grounds on the northern Labrador Shelf.     Published in Biogeosciences in 2024: https://bg.copernicus.org/articles/21/5407/2024/ <a href="https://bg.copernicus.org/articles/21/5407/2024/">BG - Characterizing regional oceanography and bottom environmental conditions at two contrasting sponge grounds on the northern Labrador Shelf</a> DOI : https://doi.org/10.5194/bg-21-5407-2024 Abstract:  Deep-sea sponge grounds are distributed globally and are considered hotspots of biological diversity and biogeochemical cycling. To date, little is known about the environmental conditions that allow high sponge biomass to develop in the deep sea. Here, we characterize oceanographic conditions at two contrasting sites off the northern Labrador Shelf with high- and low-sponge-biomass. Data were collected by year-long benthic lander deployments equipped with current meters, a turbidity and chlorophyll-a measuring device, and a sediment trap. Additionally, regional oceanography was described by analyzing vertical conductivity-temperature-depth (CTD) casts, Argo float profiles, and surface buoy drifter data for the northern Labrador Shelf from 2005 to 2022. Stable isotopic composition of benthic fauna was determined to investigate food web structure at the sponge grounds. Our results revealed strong (0.26 ± 0.14 m s-1; mean ± SD) semidiurnal tidal currents at the high-sponge-biomass site, but twofold weaker currents (0.14 ± 0.08 m s-1; mean ± SD) at the low-sponge-biomass site. Tidal analysis suggests that, at the high-sponge-biomass site, kinetic energy is dissipated from barotropic tide to baroclinic tide/turbulence, which could enhance food availability for benthic organisms. Bottom nutrient concentrations were elevated at the high-sponge-biomass site which would benefits growth in deep-sea sponges. Organic matter flux to the seafloor was increased at the high-sponge-biomass site and consisted of fresher material. Finally, both sponge grounds demonstrated tight benthic-pelagic coupling prior to the onset of stratification. Stable isotope signatures indicated that soft corals (Primnoa resedaeformis) fed on suspended particulate organic matter, while massive sponges (Geodia spp.) likely utilized additional food sources. Our results imply that benthic fauna at the high-sponge-biomass site benefit from strong tidal currents, which increases food supply, and favourable regional ocean currents that increase nutrient concentration in bottom waters.

opencc-zeroFeb 2020View details →

Experimental manipulation of perceived predation risk and cortisol generates contrasting trait trajectories in plastic crucian carp

Most animals constitute potential prey and must respond appropriately to predator-mediated stress in order to survive. Numerous prey also adaptively tailor their response to the prevailing level of risk and stress imposed by their natural enemies, i.e. they adopt an inducible defence strategy. Predator exposure may activate the stress axis, and drive the expression of anti-predator traits that facilitate survival in a high-risk environment (the predation–stress hypothesis). Here, we quantified two key morphological anti-predator traits, body morphology and coloration in crucian carp following exposure (or not) to a predator (pike) as well as to experimental manipulation of physiological stress via implants containing either cortisol or a cortisol inhibitor. We found that predator-exposed fish expressed a deeper-bodied phenotype and darker body coloration as compared with non-exposed individuals. Skin analyses revealed that an increase in the amount of melanophores caused the dramatic colour change in predatorexposed fish. Increased melanization is costly, and the darker body coloration may act as an inducible defence against predation, via a conspicuous signal of the morphological defence or by crypsis towards dark environments and a nocturnal lifestyle. By contrast, the phenotype of individuals carrying cortisol implants did not mirror the phenotype of predator-exposed fish but instead exhibited opposite trajectories of trait change: a shallow-bodied morphology with a lighter body coloration as compared with sham-treated fish. The cortisol inhibitor did not influence the phenotype of fish i.e. neither body depth nor body coloration differed between this group and predator-exposed fish having a sham implant. However, our results illuminate a potential link between stress physiology and morphological defence expression.

opencc-zeroJun 2021View details →

Local climate adaptation and gene flow in the native range of two co-occurring fruit moths with contrasting invasiveness

Invasive species pose increasing threats to global biodiversity and ecosystems. While previous studies have characterized successful invaders from ecological traits, characteristics related to evolutionary processes have rarely been investigated. Here we compared gene flow and local adaptation using demographic analyses and outlier tests in two co-occurring moth pests across their common native range of China, one of which (the peach fruit moth, Carposina sasakii) has maintained its native distribution, while the other (the oriental fruit moth, Grapholita molesta) has expanded its range globally during the past century. We found that both species showed a pattern of genetic differentiation and an evolutionary history consistent with a common southwestern origin and northward expansion in their native range. However, for the noninvasive species, genetic differentiation was closely aligned with the environment, and there was a relatively low level of gene flow, whereas in the invasive species, genetic differentiation was associated with geography. Genome scans indicated stronger patterns of climate-associated loci in the noninvasive species. While strong local adaptation and reduced gene flow across its native range may have decreased the invasiveness of C. sasakii, this requires further validation with additional comparisons of invasive and non-invasive species across their native range.

opencc-zeroJun 2021View details →

Contrasting patterns of phylogenetic diversity and alpine specialization across the alpine flora of the American mountain range system

Although mountainous habitats contribute substantially to global biodiversity, comparatively little is known about biogeographic patterns of distributions of alpine species across multiple mountain ranges. Here, we present a detailed analysis of the distributions and phylogenetic affinities of alpine seed plant lineages across North, Central, and South American mountain systems. Using a comprehensive dataset that characterized the elevational niches of American seed plants in a continuously valued way, we were able to quantitatively investigate how the proportion of alpine habitat occupied by plants related to their biogeographic distributions at a regional scale and place these results in a phylogenetic context. We found alpine species diversity to be greatest in the central Andes and western North America, and that sites with lower phylogenetic diversity contained species with a greater degree of alpine specialization. In particular, near Arctic/ boreal alpine communities were characterized by low phylogenetic diversity and higher degrees of alpine specialization, whereas the opposite was observed for southern Patagonian communities. These results suggest that abiotic filtering alone in these climatically similar regions is unlikely to explain alpine community assembly. Nevertheless, the overall relative rarity of alpine specialists, and the tendency for such specialists to be most closely related to montane lineages, suggested that filtering was still an important factor in shaping alpine community structure. This work corroborates the importance of a nuanced and scale-dependent perspective on the 'history-filtering' debate axis, as both factors have likely contributed to modern biodiversity patterns observed in alpine plant communities across the Americas.

opencc-zeroJul 2021View details →

Genomic data from the Brazilian sibilator frog reveals contrasting Pleistocene dynamics and regionalism in two South American dry biomes

Aim: Knowledge about the Neotropical dry formations, particularly the Caatinga, remains rudimentary compared to other biotas in the region. Here we address several biogeographical hypotheses by combining intense geographic and genomic sampling obtained for the Brazilian sibilator frog. We specifically test predictions related to the putative roles of past climate shifts (Pleistocene and Holocene) and local geographic barriers (past and current courses of the São Francisco river, SFR) in causing population differentiation in this species. Location: Caatinga and eastern Cerrado. Taxon: Brazilian sibilator frog Leptodactylus troglodytes. Methods: We sequenced up to ~15,000 single nucleotide polymorphisms for 159 samples from 61 locations. We inferred genetic structure using spatial clustering and examined population sizes through time. We estimated the relationship among populations using phylogenetic reconstruction, estimated historical distributions with ecological niche modelling, and inferred demographic history under isolation-with-migration models. Results: Genetic diversity in L. troglodytes corresponds to biome boundaries, with one population in the Cerrado and two populations in the Caatinga, separated by the SFR. Demographic model selection indicates the Caatinga populations expanded since the end of the Pleistocene while the Cerrado population declined. Within the Caatinga, population expansion began earlier and was more extreme in the north. A continuous stability area maintained the two Caatinga populations, which share a common origin and began diverging in the mid-Pleistocene, first with symmetric gene flow and later under pronounced migration from the north. Main Conclusions: We could not reject a role of past climate change in causing diversification of relictual populations in the Cerrado, but we found no evidence of multiple refuges or long-term isolation within the Caatinga. Instead, diversification in this biome appears to be caused by the SFR acting as a "soft barrier" that constrains migration over an extended period of time.