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Dataset results
16 results for “tree visualization”
Visual Counts of Tree Reproduction near NEON plots at Harvard Forest since 2020
Mast seeding, a resource pulse that has cascading effects in the environment, is a measure that can provide insight into forest dynamics. When masting data is collected in sequential years it can provide information on how tree populations are responding to climatic and environmental variables, and can also be used to relate to other indices, such as seed-eating animal species. The objective of this study is to quantify the yearly seed production of mast seeding tree species at Harvard Forest which are located near National Ecological Observatory Network (NEON) plots. This project is part of larger NEON-enabled project examining mast seeding on a continental scale at 25 NEON sites in the United States, which uses mast seeding records in conjunction with NEON collected data products like mammal box-trapping, tick drags, and bird point counts. Data collected on mast seeding can be linked to these other indices at regional and continental scales.
Fig. 1 in TreePics: visualizing trees with pictures
Fig. 1. Screenshot of the page with tree visualizations and associated images, showing the phylogenetic trees and the associated thumbnails. The selected thumbnails (red squares) also appear in the list below the tree.
Data from: PlaceMyFossils: An integrative approach to analyse and visualize the phylogenetic placement of fossils using backbone trees
Open the record for dataset details and reuse information.
Fig. 2 in TreePics: visualizing trees with pictures
Fig. 2. Screenshot of the page with the specimens selected on the previous page.
Visualizing reconstructed tree models
<p>Visualization on how a point cloud is created by a terrestrial laser scanner, and how a reconstructed quantitative structure model can be visualized in various ways. The visualization can be a cylinder model as shown in previous videos, but it can also be converted to a more continuous Bézier surface. The video also shows how the tree model can be augmented with non-intersecting leaves by sampling a certain distribution based on the branching structure. Both the branches and the leaves can be textured either for realism or something totally different.</p> <p>This animation was produced by the Inverse Problems research group in the Department of Mathematics at Tampere University of Technology (http://math.tut.fi/inversegroup).</p> <p>Animation created using Blender (http://www.blender.org).</p> <p>Music:<br> "Vanes" by Kevin MacLeod (http://incompetech.com)<br> Licensed under Creative Commons: By Attribution 3.0<br> http://creativecommons.org/licenses/by/3.0/</p> <p>Textures:<br> "Bark 0007"<br> xoio (xoio.de)</p> <p>"Cherry Leaf"<br> BrianHanson2nd (deviantart.com)<br> Licensed under Creative Commons: By Attribution 3.0<br> http://creativecommons.org/licenses/by/3.0/</p> <p>The animation builds upon but does not directly feature the "Prunus avium - Cherry Tree" point cloud data by Jan Hackenberg (http://www.simpletree.uni-freiburg.de/openData.html) shared under the Creative Commons - Attribution-NonCommercial-ShareAlike 4.0 International license<br> http://creativecommons.org/licenses/by-nc-sa/4.0/</p>
Manuscript data for "Iroki: automatic customization and visualization of phylogenetic trees"
<p>Manuscript data for "Iroki: automatic customization and visualization of phylogenetic trees"</p>
Figure 3 in In front of a mirror: visual displays may not be aggressive signals in nocturnal tree frogs
Figure 3. Rate of vocal-sac (emission time/total time), limb lifting (events/min) and toe/finger trembling (events/min) displays by males of Hypsiboas raniceps (n = 6), Dendropsophus nanus (n = 6) and Lysapsus limellum (n = 5) subjected to two treatments (Self Image and Control) in the southeastern Pantanal, Corumbá, state of Mato Grosso do Sul, Brazil. Toe/finger trembling behaviour was performed only by males of H. raniceps during the experiments. Each pair of points represents one individual; and points may overlap each other. The frequency of behaviours did not differ, either between treatments or among species.
Figure 1 in In front of a mirror: visual displays may not be aggressive signals in nocturnal tree frogs
Figure 1. Males of (a) Hypsiboas raniceps, (b) Dendropsophus nanus and (c) Lysapsus limellum located in the southeastern Pantanal, Corumbá, state of Mato Grosso do Sul, Brazil. Note that all males perform the vocal-sac display behaviour (inflate the vocal sac, with or without vocalization, and maintain it inflated for some time).
Figure 2 in In front of a mirror: visual displays may not be aggressive signals in nocturnal tree frogs
Figure 2. Self Image treatment applied to a male of Hypsiboas raniceps in the southeastern Pantanal, Corumbá, state of Mato Grosso do Sul, Brazil. The reflection of the animal in the mirror (14 × 8 cm), positioned at an angle of approximately 45° in relation to the male's body position, simulated the presence of an intruder male in the resident's territory.
Figure 4. ITS1 gene tree. Terminal tips have been collapsed for visualization purposes. Nodes are labelled with ultrafast bootstrap support. A in Hidden in the hills: phylogeny of the freshwater mussel genus Alasmidonta (Bivalvia: Unionidae) and description of a new species
Figure 4. ITS1 gene tree. Terminal tips have been collapsed for visualization purposes. Nodes are labelled with ultrafast bootstrap support. A full tree is available in the Supporting Information (File S1). The scale is in substitutions per site.
Visualization of the Extrahepatic biliaRy Tree Trial
ClinicalTrials.gov study NCT04922528. IPD Sharing: NO. Countries: 1. Publications: 2.
Fluorescence Versus Intraoperative Cholangiography in the Visualization of Biliary Tree Anatomy
ClinicalTrials.gov study NCT01881399. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Data from: ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data
We present an r package, ggtree, which provides programmable visualization and annotation of phylogenetic trees. ggtree can read more tree file formats than other softwares, including newick, nexus, NHX, phylip and jplace formats, and support visualization of phylo, multiphylo, phylo4, phylo4d, obkdata and phyloseq tree objects defined in other r packages. It can also extract the tree/branch/node-specific and other data from the analysis outputs of beast, epa, hyphy, paml, phylodog, pplacer, r8s, raxml and revbayes software, and allows using these data to annotate the tree. The package allows colouring and annotation of a tree by numerical/categorical node attributes, manipulating a tree by rotating, collapsing and zooming out clades, highlighting user selected clades or operational taxonomic units and exploration of a large tree by zooming into a selected portion. A two-dimensional tree can be drawn by scaling the tree width based on an attribute of the nodes. A tree can be annotated with an associated numerical matrix (as a heat map), multiple sequence alignment, subplots or silhouette images. The package ggtree is released under the artistic-2.0 license. The source code and documents are freely available through bioconductor (http://www.bioconductor.org/packages/ggtree).
Data from: ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data
Open the record for dataset details and reuse information.
FIGURE 19. Mapped COI gene tree. COI barcode tree from Fig. 18 visualized against a in Thirteen new species of Chilecicada Sanborn, 2014 (Hemiptera: Auchenorrhyncha: Cicadidae: Tibicininae) expand the highly endemic cicada fauna of Chile
FIGURE 19. Mapped COI gene tree. COI barcode tree from Fig. 18 visualized against a map of specimen localities using web application TreeToM (See methods). Colors represent described species.
AnnoTree: visualization and exploration of protein domain families across the tree of life
<p>This file is an older version of AnnoTree, published before BioArxiv first print, please do not use.</p>
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research 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.
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.
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.
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.
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.