Find research datasets worth reusing

Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.

datasets available to search

ShareScore release 0.9.0

Dataset results

24 results for “Data for analysis of shape”

Learn how ShareScore rates datasets ↗

dryad40/100

Data and analysis from: Body mass, temperature, and depth shape the maximum intrinsic rate of population increase in sharks and rays

An important challenge in ecology is to understand variation in species' maximum intrinsic rate of population increase, 𝑟𝑚𝑎𝑥, not least because 𝑟𝑚𝑎𝑥 underpins our understanding of the limits of fishing, recovery potential, and ultimately extinction risk. Across many vertebrate species, terrestrial and aquatic, body mass and environmental temperature are important correlates of 𝑟𝑚𝑎𝑥. In sharks and rays, specifically, 𝑟𝑚𝑎𝑥 is known be lower in larger species, but also in deep-sea ones. We use an information-theoretic approach that accounts for phylogenetic relatedness to evaluate the relative importance of body mass, temperature and depth on 𝑟𝑚𝑎𝑥. We show that both temperature and depth have separate effects on shark and ray 𝑟𝑚𝑎𝑥 estimates, such that species living in deeper waters have lower 𝑟𝑚𝑎𝑥. Furthermore, temperature also correlates with changes in the mass scaling coefficient, suggesting that as body size increases, decreases in 𝑟𝑚𝑎𝑥 are much steeper for species in warmer waters. These findings suggest that there are (as-yet understood) depth-related processes that limit the maximum rate at which populations can grow in deep sea sharks and rays. While the deep ocean is associated with colder temperatures, other factors that are independent of temperature, such as food availability and physiological constraints, may influence the low 𝑟𝑚𝑎𝑥 observed in deep sea sharks and rays. Our study lays the foundation for predicting the intrinsic limit of fishing, recovery potential, and extinction risk species based on easily accessible environmental information such as temperature and depth, particularly for data-poor species. This repository contains the data and a minimum working example of the model-fitting process used for the article "Body mass, temperature, and depth shape productivity in sharks and rays", which is currently in press at Ecology and Evolution.

opencc-zeroOct 2022View details →

zenodo40/100

Synthetic Data for Neutrophil Analysis: Sets with irregular shapes and Poisson noise

Synthetic Datasets with irregular shapes and Poisson noise. Part of the PhagoSight neutrophil tracking and analysis package (Henry, et al., PLOS ONE, 2013):   https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0072636 http://www.phagosight.org https://github.com/phagosight/phagosight   A series of synthetic data sets that reproduce different behaviour characteristics of migrating neutrophils were generated in MATLAB. The data sets consisted of six artificial neutrophils that travelled along paths that presented different conditions of tortuosity, times to activation and proximity to other neutrophils during 98 time frames. Numerous data sets of neutrophils in zebrafish were carefully observed before setting the characteristics. Six trajectories were manually determined by setting the row, column positions of the centroids at every time point for 98 time frames. Each trajectory was designed so that it would represent different neutrophil behaviours: some trajectories were very oriented and had movements with uniform distance between time frames, whilst others were less uniform and would move at different velocities, some were tortuous whilst others were straight. The trajectories of cells 1 and 2 collided several times in the second half of the time frames whilst cells 3 and 4 collided at the beginning of the movement. Cell 6 migrated without meandering and then stopped at the end (which represents the wound area of an inflammation-based experiment) whilst 5 presented a delayed activation.  Each time frame consisted of 11 slices of z-stack each with 275 x 275 pixels, where the neutrophils were formed by irregular shapes (sum of Gaussians) and Poisson Noise (check the corresponding sets with regular shapes, i.e. Gaussians with Gaussian noise plus another set with a single large neutrophil and Poisson noise) distributions of higher intensities than the background. The orientation of the Poisson varied according to the displacement of the artificial neutrophils, i.e.they were round when the cells were static, or elongated when in movement. The tracks with the Shapes were saved as the gold standard and five different data sets were generated by adding varying levels of white Poisson noise resulting in data sets with distributions with increasing similarity between the neutrophils and the background reflected by the decreasing values of the Bhattacharyya Distance (1.61, 1.25, 1, 0.66, 0.45) as defined by Coleman 1979.   Files corresponding to the sets with irregular shapes and Poisson noise (noise increases from 1 to 5): <ul> <li>    x,y,t trajectories    ThreeDTracks</li> <li>    Ground Truth       syntheticData_P_mat_La </li> <li>    First data set         syntheticData_P1_mat_Re</li> <li>    Second data set     syntheticData_P2_mat_Re</li> <li>    Third data set       syntheticData_P3_mat_Re</li> <li>    Fourth data set     syntheticData_P4_mat_Re</li> <li>    Fifth data set        syntheticData_P5_mat_Re</li> </ul> Corresponding GIF files are also included as illustrations of the cells in motion.   Main Reference: <a href="https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0072636">PhagoSight: An Open-Source MATLAB® Package for the Analysis of Fluorescent Neutrophil and Macrophage Migration in a Zebrafish Model </a> Henry KM, Pase L, Ramos-Lopez CF, Lieschke GJ, Renshaw SA, Reyes-Aldasoro CC. (2013) PhagoSight: An Open-Source MATLAB® Package for the Analysis of Fluorescent Neutrophil and Macrophage Migration in a Zebrafish Model. PLOS ONE 8(8): e72636. <a href="https://doi.org/10.1371/journal.pone.0072636">https://doi.org/10.1371/journal.pone.0072636</a>

opencc-by-4.0Apr 2013View details →

zenodo40/100

Synthetic Data for Neutrophil Analysis: Sets with regular shapes and Gaussian noise

Synthetic Datasets with regular shapes and Gaussian noise. Part of the PhagoSight neutrophil tracking and analysis package (Henry, et al., PLOS ONE, 2013):   https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0072636 http://www.phagosight.org https://github.com/phagosight/phagosight   A series of synthetic data sets that reproduce different behaviour characteristics of migrating neutrophils were generated in MATLAB. The data sets consisted of six artificial neutrophils that travelled along paths that presented different conditions of tortuosity, times to activation and proximity to other neutrophils during 98 time frames. Numerous data sets of neutrophils in zebrafish were carefully observed before setting the characteristics. Six trajectories were manually determined by setting the row, column positions of the centroids at every time point for 98 time frames. Each trajectory was designed so that it would represent different neutrophil behaviours: some trajectories were very oriented and had movements with uniform distance between time frames, whilst others were less uniform and would move at different velocities, some were tortuous whilst others were straight. The trajectories of cells 1 and 2 collided several times in the second half of the time frames whilst cells 3 and 4 collided at the beginning of the movement. Cell 6 migrated without meandering and then stopped at the end (which represents the wound area of an inflammation-based experiment) whilst 5 presented a delayed activation.  Each time frame consisted of 11 slices of z-stack each with 275 x 275 pixels, where the neutrophils were formed by Gaussian distributions of higher intensities than the background and Gaussian noise (check the corresponding irregular shapes with Poisson noise plus another set with a single large neutrophil and Poisson noise). The orientation of the Gaussians varied according to the displacement of the artificial neutrophils, i.e.they were round when the cells were static, or elongated when in movement. The tracks with the Gaussians were saved as the gold standard and five different data sets were generated by adding varying levels of white Gaussian noise resulting in data sets with distributions with increasing similarity between the neutrophils and the background reflected by the decreasing values of the Bhattacharyya Distance (1.61, 1.25, 1, 0.66, 0.45) as defined by Coleman 1979.   Files corresponding to the sets with irregular shapes and Poisson noise (noise increases from 1 to 6): <ul> <li>    x,y,t trajectories    ThreeDTracks</li> <li>    Ground Truth       syntheticData0_mat_Re </li> <li>    First data set         syntheticData1_mat_Re</li> <li>    Second data set     syntheticData2_mat_Re</li> <li>    Third data set       syntheticData3_mat_Re</li> <li>    Fourth data set     syntheticData4_mat_Re</li> <li>    Fifth data set         syntheticData5_mat_Re</li> <li>    Sixth data set         syntheticData6_mat_Re</li> </ul>   Corresponding GIF files are also included as illustrations of the cells in motion.   Main Reference: <a href="https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0072636">PhagoSight: An Open-Source MATLAB® Package for the Analysis of Fluorescent Neutrophil and Macrophage Migration in a Zebrafish Model </a> Henry KM, Pase L, Ramos-Lopez CF, Lieschke GJ, Renshaw SA, Reyes-Aldasoro CC. (2013) PhagoSight: An Open-Source MATLAB® Package for the Analysis of Fluorescent Neutrophil and Macrophage Migration in a Zebrafish Model. PLOS ONE 8(8): e72636. <a href="https://doi.org/10.1371/journal.pone.0072636">https://doi.org/10.1371/journal.pone.0072636</a>

opencc-by-4.0Apr 2013View details →

dryad40/100

Data and analysis scripts for: Co-occurrence patterns at four spatial scales implicate reproductive processes in shaping community assembly in clovers

Open the record for dataset details and reuse information.

publicSep 2021View details →

dryad40/100

Data and analysis from: Body mass, temperature, and depth shape the maximum intrinsic rate of population increase in sharks and rays

Open the record for dataset details and reuse information.

publicOct 2022View details →

dryad36/100

Data from: Comparative analysis of the shape and size of the middle ear cavity of turtles reveals no correlation with habitat ecology

The middle ear of turtles differs from other reptiles in being separated into two distinct compartments. Several ideas have been proposed as to why the middle ear is compartmentalized in turtles, most suggesting a relationship with underwater hearing. Extant turtle species span fully marine to strictly terrestrial habitats, and ecomorphological hypotheses of turtle hearing predict that this should correlate with variation in the structure of the middle ear due to differences in the fluid properties of water and air. We investigate the shape and size of the air-filled middle ear cavity of 56 extant turtles using 3D data and phylogenetic comparative analysis to test for correlations between habitat preferences and the shape and size of the middle ear cavity. Only weak correlations are found between middle ear cavity size and ecology, with aquatic taxa having proportionally smaller cavity volumes. The middle ear cavity of turtles exhibits high shape diversity among species, but we found no relationship between this shape variation and ecology. Surprisingly, the estimated acoustic transformer ratio, a key functional parameter of impedance-matching ears in vertebrates, also shows no relation to habitat preferences (aquatic/terrestrial) in turtles. We suggest that middle ear cavity shape may be controlled by factors unrelated to hearing, such as the spatial demands of surrounding cranial structures. A review of the fossil record suggests that the modern turtle ear evolved during the Early to Middle Jurassic in stem turtles broadly adapted to freshwater and terrestrial settings. This, combined with our finding that evolutionary transitions between habitats caused only weak evolutionary changes in middle ear structure, suggests that tympanic hearing in turtles evolved as a compromise between subaerial and underwater hearing.

opencc-zeroAug 2019View details →

zenodo36/100

Data for geometric analysis of seed shape diversity in the Cucurbitaceae

Data to complement the article Geometric analysis of seed shape diversity in the Cucurbitaceae

opencc-by-4.0Nov 2023View details →

dryad36/100

Data from: Comparative analysis of the shape and size of the middle ear cavity of turtles reveals no correlation with habitat ecology

Open the record for dataset details and reuse information.

publicAug 2019View details →

zenodo32/100

statistical analysis and data: How personality shapes gaze behavior without compromising subtle emotion recognition.

<pre>CODE: script_gca_X.R: scripts used for the growth curve analysis fits script_fits_brms_no_tb.r: script containing the fits (except those related to the crowth curve analysis). inpact_script_contrasts.r: contrasts of every fits (call inpact_script_plot.r and inpact_script_save.r) inpact_script_plot.r: plots inpact_script_save: save contrasts to csv and xlsx files DATA: cluster_df.Rda: personality neutral.Rda: neutral trials sdtg.Rda: signal detection theory parameters resp_emo.Rda : raw data to emotional trials df_et4_propn.Rda: eye tracking data, first exposure phase of the emotional trials (0-1000ms) df_et4_prop.Rda: eye tracking data, second exposure phase of the emotional trials (1000-2000ms) df_n4_propn.Rda: eye tracking data, first exposure phase of the neutral trials (0-1000ms) df_n4_prop.Rda: eye tracking data, second exposure phase of the neutral trials (1000-2000ms) gca_e_contrast.Rda: contrasts of the growth curve analysis fit for the eye Area of Interest (AOI) gca_n_contrast.Rda: contrasts of the growth curve analysis fit for the nose AOI gca_m_contrast.Rda: contrasts of the growth curve analysis fit for the mouth AOI X.rds: fits STIMULI: - videos of the neutral and emotional facial expressions - backward masks</pre>

opencc-by-4.0Sep 2024View details →

zenodo32/100

Data supporting the analysis of lymphatic endothelial cell junctions and shape

Data in support of:  Dynamic cytoskeletal regulation of cell shape supports resilience of lymphatic endothelium Hans Schoofs1#, Nina Daubel1#, Sarah Schnabellehner1, Max Grönloh2, Sebastián Palacios Martínez3, Aleksi Halme4, Amanda M. Marks1, Marie Jeansson1, Sara Barcos5, Cord Brakebusch6, Rui Benedito7, Britta Engelhardt5, Dietmar Vestweber8, Konstantin Gängel1, Fabian Linsenmeier9, Sebastian Schürmann9, Pipsa Saharinen4,10, Jaap D. van Buul2,3,11, Oliver Friedrich9, Richard S. Smith12, Mateusz Majda13, and Taija Mäkinen1,4,10*   1Uppsala University, Department of Immunology, Genetics and Pathology, Dag Hammarskjölds väg 20, 751 85 Uppsala, Sweden. 2Department of Medical Biochemistry at the Amsterdam UMC, location AMC, The Netherlands. 3Department of Molecular Cytology, Leeuwenhoek Centre for Advanced Microscopy at Swammerdam Institute for Life Sciences at the University of Amsterdam, The Netherlands. 4Translational Cancer Medicine Program and Department of Biochemistry and Developmental Biology, University of Helsinki, Haartmaninkatu 8, 00014 Helsinki, Finland. 5Theodor Kocher Institute, University of Bern, Bern, Switzerland. 6Biotech Research and Innovation Center, University of Copenhagen, Ole Maaløes Vej 5, 2200 Denmark. 7Centro Nacional de Investigaciones Cardiovasculares, Melchor Fernández Almagro 3, E-28029 Madrid, Spain. 8Max Planck Institute for Molecular Biomedicine, Münster, Germany. 9Institute of Medical Biotechnology, Department of Chemical and Biological Engineering, Friedrich-Alexander-University, Erlangen-Nürnberg, Paul-Gordan-Str.3, 91052 Erlangen, Germany. 10Wihuri Research Institute, Haartmaninkatu 8, 00290 Helsinki, Finland. 11Amsterdam UMC, Sanquin Research and Landsteiner Laboratory, The Netherlands. 12John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK. 13Department of Plant Molecular Biology, University of Lausanne, CH-1015 Lausanne, Switzerland. #These authors contributed equally. *Corresponding author: Taija Mäkinen, E-mail: <a href="mailto:taija.makinen@igp.uu.se">taija.makinen@igp.uu.se</a>, <a href="mailto:taija.makinen@helsinki.fi">taija.makinen@helsinki.fi</a>   DATASET A: Annotated cell-cell junction types in lymphatic capillaries of wild type mouse ear skin at different ages  __________________________________________________________________________________________________________ Contents <ul> <li>SOURCE DATA Fig1 FINAL. xlsx</li> <li>3w <ul> <li>animal 1</li> <li>animal 2</li> <li>animal 3</li> <li>animal 4</li> <li>animal 5</li> <li>sprouts</li> </ul> </li> <li>5w <ul> <li>animal 1</li> <li>animal 2</li> <li>animal 3</li> <li>animal 4</li> <li>animal 5</li> <li>diaphragm <ul> <li>Overview of diaphragm and high mag. of different capillary ends</li> </ul> </li> <li>trachea</li> </ul> </li> <li>25w <ul> <li>animal 1</li> <li>animal 2</li> <li>animal 3</li> <li>animal 4</li> <li>animal 5</li> <li>diaphragm</li> <li>trachea</li> </ul> </li> </ul> File legends C1 images: inverted LYVE1 signal (.tif) C2 images: inverted VE-cadherin signal (.tif) MAX images: RGB merge of LYVE1 (cyan) and VE-cadherin (red) (.tif) "NAME".roi: Regions of interest (ROI) of annotated junctions can be imported in ImageJ Methods Junctional classification:  Analysis of junction morphology was done on blunt-ended initial lymphatic capillaries in the segment between the intial tip and the first valve. Junction types were quantified in Z-stack projection by numbering of individual lobes of LYVE1 and VE-cadherin-stained LECs and subsequent categorizing of lobe-associated junctions based on VE-cadherin signal. Four categories were defined: 1) Button junction – a punctate VE-cadherin+ deposit at the neck of LYVE1+ lobe/overlap, with no detectable VE-cadherin at the borders of the overlap, 2) Curvilinear junction – unsegmented(continous) or segmented (discontinuous) distribution of VE-cadherin within one border of LYVE1+ lobe/cellular overlap, 3) Double junction – unsegmented(continous) or segmented (discontinuous) distribution of VE-cadherin within both borders of LYVE1+ lobe/cellular overlap, and 4) LYVE1- curvilineair junction – unsegmented(continous) linear VE-cadherin distribution at cell-cell contacts in the absence of LYVE1. Wild-type C57BL/6J mice were used for analysis of junction types, and 4-5 blunt ended vessels per mouse from five mice per age group and condition were analysed; in total 1785 junctions were annoted Imaging: Confocal images were obtained using a Leica Stellaris 5 confocal microscope equipped with 405 nm and white light lasers, 63x/1.3 HC PL APO CORR CS2 Glycerol immersion objective, and Leica LAS X software. Images were aquired at 1.51 digital zoom using a 2048x2048 resolution Tissue processing and staining:   Tissues were fixed in 4% paraformaldehyde for 2 h at RT and permeabilized in 0.3% Triton X-100 in PBS (PBST) for 10 min. After blocking in PBST with 2% bovine serum albumin, 1% FBS for 2 h, tissues were incubated with primary antibodies in blocking buffer overnight, followed by PBST washing and incubation with fluorescent dye-conjugated secondary antibodies for 2 h. All incubation steps were carried out at RT. Prior to mounting in Mowiol, samples were repeatedly washed in PBST and water. Antibodies used: Goat anti-mouse VE-cadherin (R&D Systems, AF1002; 1:200), Rat anti-mouse LYVE1 (R&D Systems, MAB2125; 1:200)   DATASET B: Finite element method (FEM) simulations of cellular stresses _______________________________________________________________ The FEM simulations were performed with MorphoMechanX using available models adapted from Sapala et al, eLife 7, e32794 (2018). A regular cylindrical grid 45 µm wide and 200 µm long was created and outlines from the cells of a lymphatic vessel were projected onto it and smoothed. These cells were then extruded inward to make 3D volumetric cells with a depth of 2 µm and triangulated using a threshold area of 4 µm.  The template was then used as the reference configuration for triangular 3 node membrane elements which were given a thickness of 0.1um. An isotropic St. Venant material model (linear, large deformation) was used with the Young's modulus set to 100 kPa to match a 10 kPa cell level Young's modulus estimated from the literature (ignoring the cell ends, the 2 x 0.1 µm membrane thickness occupied roughly 1/10th the cross-sectional area of the cell that were 2 µm deep). A uniform internal pressure was applied normal to the inside faces of the elements, which cancels out on the shared walls between cells. For simulations with a lower pressure inside the vessel, the inside faces were assigned a higher pressure. Stresses were visualized as the trace of the stress tensor.

opencc-by-4.0Apr 2024View details →

zenodo32/100

Data for GLM analysis of "How thermal priming of coral gametes shapes fertilization success"

Data, self-explanatory, used to conduct the GLM analysis and obtain the results presented in the article "How thermal priming of coral gametes shapes fertilization success" by Antoine Puisay, Laetitia Hédouin, Rosanne Pilon, Claire Goiran, and Benoit Pujol, published in Journal of Experimental Biology and Ecology

opencc-by-4.0Jun 2023View details →

dryad32/100

Data from: BMI and WHR are reflected in female facial shape and texture: a geometric morphometric image analysis

Open the record for dataset details and reuse information.

publicDec 2017View details →

dryad32/100

Data from: Multi-locus analysis of Pristionchus pacificus on La Réunion Island reveals an evolutionary history shaped by multiple introductions, constrained dispersal events, and rare out-crossing

Open the record for dataset details and reuse information.

publicOct 2011View details →

zenodo28/100

Data associated with "Adjoint methods for stellarator shape optimization and sensitivity analysis"

All data produced for this dissertation and the associated post-processing scripts have been archived.

opencc-by-4.0Mar 2020View details →

dryad28/100

Data from: Quantitative genetic analysis of subspecific differences in body shape in the snail-feeding carabid beetle Damaster blaptoides

A dimorphic pattern of macrocephalic (wide, short) and stenocephalic (narrow, long) body shapes is observed in snail-feeding carabid beetles globally. The former exhibits high performance in crushing snail shells with powerful jaws, whereas the latter specializes in eating snails' soft body directly by inserting the head into the shell. In the snail-feeding species Damaster blaptoides, the subspecies D. b. capito has a wide short forebody, and D. b. fortunei has a narrow, long forebody. They exhibit distinct morphologies despite their geographic and phylogenetic proximity. To examine the genetic basis of the morphological differences between these two subspecies, we conducted quantitative genetic analyses by crossing these subspecies and producing F_1 and backcross hybrids. The hybrids had body shapes intermediate between the parental subspecies. The variation between wide, short and narrow, long forebodies was based on negative geneti c correlations between width and length of the head and thorax. Between one and eight genetic factors were involved in the morphological differences between subspecies. We suggest that the morphological integration of forebody parts in a small number of loci has facilitated the marked morphological diversification between subspecies of D. blaptoides.

opencc-zeroDec 2011View details →

dryad28/100

Data from: Shape analysis of moss (Bryophyta) sporophytes: insights into land plant evolution

PREMISE OF THE STUDY: The alternation of generations life cycle represents a key feature of land-plant evolution and has resulted in a diverse array of sporophyte forms and modifications in all groups of land plants. We test the hypothesis that evolution of sporangium (capsule) shape of the mosses—the second most diverse land-plant lineage—has been driven by differing physiological demands of life in diverse habitats. This study provides an important conceptual framework for analyzing the evolution of a single, homologous character in a continuous framework across a deep expanse of time, across all branches of the tree of life. METHODS: We reconstruct ancestral sporangium shape and ancestral habitat on the largest phylogeny of mosses to date, and use phylogenetic generalized least squares regression to test the association between habitat and sporangium shape. In addition, we examine the association between shifts in sporangium shape and species diversification. RESULTS: We demonstrate that sporangium shape is convergent, under natural selection, and associated with habitat type, and that many shifts in speciation rate are associated with shifts in sporangium shape. CONCLUSIONS: Our results suggest that natural selection in different microhabitats results in the diversity of sporangium shape found in mosses, and that many increasing shifts in speciation rate result in changes in sporangium shape across their 480 million year history. Our framework provides a way to examine if diversification shifts in other land plants are also associated with massive changes in sporophyte form, among other morphological traits.

opencc-zeroDec 2015View details →

dryad28/100

Data from: Shape analysis of symmetric structures: quantifying variation among individuals and asymmetry

Morphometric studies often consider parts with internal left-right symmetry, for instance, the vertebrate skull. This type of symmetry is called object symmetry and is distinguished from matching symmetry, in which two separate structures exist as mirror images of each other, one on each body side. We explain a method for partitioning the total shape variation of landmark configurations with object symmetry into components of symmetric variation among individuals and asymmetry. This method is based on the Procrustes superimposition of the original and a reflected copy of each landmark configuration and is compatible with the two-factor ANOVA model customary in studies of fluctuating asymmetry. We show a fully multivariate framework for testing the effects in the two-factor model with MANOVA statistics, which also applies to shapes with matching symmetry. We apply the new methods in a small case study of pharyngeal jaws of the Neotropical cichlid fish Amphilophus citrinellus. The analysis revealed that the symmetric component of variation in the pharyngeal jaws is dominated by the contrast between two alternative trophic morphs in this species and that there is subtle but statistically significant directional asymmetry. Finally, we provide some general recommendations for morphometric studies of symmetric shapes.

opencc-zeroDec 2011View details →

dryad28/100

Data from: Facultative bacterial endosymbionts shape parasitoid food webs in natural host populations: a correlative analysis

1.Facultative bacterial endosymbionts can protect their aphid hosts from natural enemies such as hymenopteran parasitoids. As such, they have the capability to modulate interactions between aphids, parasitoids and hyperparasitoids. However, the magnitude of these effects in natural aphid populations and their associated parasitoid communities is currently unknown. Moreover, environmental factors such as plant fertilization and landscape complexity are known to affect aphid‐parasitoid interactions but it remains unclear how such environmental factors affect the interplay between aphids, parasitoids and endosymbionts. 2.Here, we tested whether facultative endosymbionts confer protection to parasitoids in natural populations of the English grain aphid, Sitobion avenae, and if this is affected by plant fertilization and landscape complexity. Furthermore, we examined whether the effects of facultative endosymbionts can cascade up to the hyperparasitoid level and increase primary‐hyperparasitoid food web specialization. 3.Living aphids and mummies were collected in fertilized and unfertilized plots within 13 wheat fields in Central Germany. We assessed the occurrence of primary parasitoid, hyperparasitoid and endosymbiont species in aphids and mummies using a newly established molecular approach. 4.Facultative endosymbiont infection rates were high across fields (~80 %), independent of whether aphids were parasitized or un‐parasitized. Aphid mummies exhibited a significantly lower share of facultative endosymbiont infection (~38 %). These findings suggest that facultative endosymbionts do not affect parasitoid oviposition behavior, but decrease parasitoid survival in the host. Facultative endosymbiont infection rates were lower in mummies collected from fertilized compared to unfertilized plants, indicating that plant fertilization boosts the facultative endosymbiont protective effect. Furthermore, we found strong evidence for species‐specific and negative cascading effects of facultative endosymbionts on primary and hyperparasitoids, respectively. Facultative endosymbionts impacted parasitoid assemblages and increased the specialization of primary‐hyperparasitoid food webs: these effects were independent from and much stronger than other environmental factors. 5.The current findings stongly suggest that facultative endosymbionts act as a driving force in aphid‐parasitoid‐hyperparastioid networks: they shape insect community composition at different trophic levels and modulate, directly and indirectly, the interactions between aphids, parasitoids and their environment.

opencc-zeroDec 2017View details →

zenodo28/100

Synthetic Data for Neutrophil Analysis: Sets one large neutrophil shape and Poisson noise

Synthetic Datasets with  one large irregular shape and Poisson noise. Part of the PhagoSight neutrophil tracking and analysis package (Henry, et al., PLOS ONE, 2013):   https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0072636 http://www.phagosight.org https://github.com/phagosight/phagosight   A series of synthetic data sets that reproduce different behaviour characteristics of migrating neutrophils were generated in MATLAB. The data sets consisted of one artificial neutrophil that travelled along a path that presented different conditions of tortuosity, times to activation during 98 time frames. Numerous data sets of neutrophils in zebrafish were carefully observed before setting the characteristics. One trajectory was manually determined by setting the row, column positions of the centroid at every time point for 98 time frames. The trajectory was designed so that it would represent different neutrophil behaviours: some moments were very oriented and had movements with uniform distance between time frames, whilst others were less uniform and would move at different velocities, some were tortuous whilst others were straight. Each time frame consisted of 11 slices of z-stack each with 275 x 275 pixels, where the neutrophil was formed by Gaussian distributions of higher intensities than the background and Poisson noise (check the corresponding sets with smaller regular shapes with Gaussian noise and irregular shapes with Poisson noise).   Files corresponding to the sets with irregular shapes and Poisson noise (noise increases from 1 to 5): <ul> <li>    Ground Truth       syntheticData_L_mat_La </li> <li>    First data set         syntheticData_L1_mat_Re</li> <li>    Second data set     syntheticData_L2_mat_Re</li> <li>    Third data set       syntheticData_L3_mat_Re</li> <li>    Fourth data set     syntheticData_L4_mat_Re</li> <li>    Fifth data set        syntheticData_L5_mat_Re</li> </ul>   Corresponding GIF files are also included as illustrations of the cells in motion.   Main Reference: <a href="https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0072636">PhagoSight: An Open-Source MATLAB® Package for the Analysis of Fluorescent Neutrophil and Macrophage Migration in a Zebrafish Model </a> Henry KM, Pase L, Ramos-Lopez CF, Lieschke GJ, Renshaw SA, Reyes-Aldasoro CC. (2013) PhagoSight: An Open-Source MATLAB® Package for the Analysis of Fluorescent Neutrophil and Macrophage Migration in a Zebrafish Model. PLOS ONE 8(8): e72636. <a href="https://doi.org/10.1371/journal.pone.0072636">https://doi.org/10.1371/journal.pone.0072636</a>

opencc-by-4.0Apr 2013View details →

dryad28/100

Data from: Shape analysis of moss (Bryophyta) sporophytes: insights into land plant evolution

Open the record for dataset details and reuse information.

publicFeb 2017View details →

ScienceDex guides

Understand access before you commit

These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.

Compare curated datasets

Allen Brain Atlas

Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.

allen-brain-atlas

neuroscienceopenDocumentation, web resources, and API references are available online.

Last verified 2026-04-30Open record

Annotated Behaviour and Observability Dataset (ABODe)

ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.

abode-home-cage

behavioral-neuroscienceopenThe DataShare record exposes download links for annotations, documentation, license text, and the zipped per-snippet data directory.

Last verified 2026-04-30Open record

DANDI Archive for NWB datasets

DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.

dandi-nwb

electrophysiologyopenPublished Dandiset metadata and archive endpoints are available through the production DANDI API.

Last verified 2026-04-30Open record

International Brain Laboratory public data

The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.

ibl

behavioral-neuroscienceopenPublic sessions can be searched and loaded from the IBL public data server through ONE.

Last verified 2026-04-29Open record

OpenNeuro

OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.

openneuro

neuroscienceopenPublished datasets are available on demand over the internet.

Last verified 2026-04-29Open record