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7,523 results for “Annotation”
Fig. 4 in Annotated review of Cryptocephalinae (Clytrini), Synetinae and part of Galerucinae (Coleoptera, Chrysomelidae) described by Carl Peter Thunberg
Fig. 4. Melitonoma decemnotata (Thunberg, 1787) comb. nov. A–E. Syntype, ♀, 5.8 mm, UUZM. A. Dorsal view. B. Lateral view. C. Frontal view. D. Labels. E. Box label. F–G. Kotpresse. F. Ventral view. G. Dorsal view. H. ♂, 6.1 mm, RSA, Worcester, BMNH. I. ♀, 5.7 mm, RSA, Worcester, BMNH. J. Male head, frontal view.
Fig. 11 in Annotated review of Cryptocephalinae (Clytrini), Synetinae and part of Galerucinae (Coleoptera, Chrysomelidae) described by Carl Peter Thunberg
Fig. 11. Protoclytra taeniata (Thunberg, 1821) comb. nov. A–E. Holotype, ♂, 8.0 mm, UUZM. A. Dorsal view. B. Lateral view. C. Frontal view. D. Label. E. Box label. F–G. Syntype of Clythra fastuosa Lacordaire, 1848, ♂, not measured, ZMHB. F. Dorsal view. G. Labels.
Fig. 13. A–D in Annotated review of Cryptocephalinae (Clytrini), Synetinae and part of Galerucinae (Coleoptera, Chrysomelidae) described by Carl Peter Thunberg
Fig. 13. A–D. Holotype of Teinocera catenata (Thunberg, 1821) comb. nov., ♂, 6.7 mm, UUZM. A. Dorsal view. B. Frontal view. C. Label. D. Box label. E–G. Syneta betulae (Fabricius, 1792) (syntype of Crioceris betulina Thunberg, 1787, unsexed, 6.0 mm, UUZM). E. Dorsal view. F. Label. G. Box label.
Fig. 10 in Annotated review of Cryptocephalinae (Clytrini), Synetinae and part of Galerucinae (Coleoptera, Chrysomelidae) described by Carl Peter Thunberg
Fig. 10. Phoenicodera scapularis (Thunberg, 1821). A–D. Syntype, ♂, 9.0 mm, UUZM. A. Dorsal view. B. Lateral view. C. Frontal view. D. Label and box label. E–G. Syntype, ♀, 7.8 mm, UUZM. E. Dorsal view. F. Label. G. Box label.
Pecha Layout Analysis Annotations in Transkibus Format
<p>Training data for <em>Layout Analysis</em> of Tibetan woodblock prints. This version of dataset contain images randomly picked images from LOC scans of the <a href="https://www.tbrc.org/#!rid=W4CZ5369">derge kangyur</a>.</p> <p><strong>Training data contains:</strong></p> <ol> <li>Text region annotations</li> <li>Line annotations</li> </ol> <p>Note: The annotations scheme is based on <a href="https://transkribus.eu/Transkribus/">Transkribus</a><strong>. </strong>Importing the annotations is same as importing an exported Transkribus format documents.</p>
Microscopy image sequences and annotated kymographs of laser ablation experiments in Drosophila embryos
<p><strong>Content</strong></p> <p>This dataset contains 15 2D time-lapse fluorescence microscopy image sequences recorded with confocal laser-scanning microscopy. Each movie shows an epithelial tissue laser nanoablation experiment conducted in a Drosophila embryo.</p> <p>For each sequence, the dataset contains kymographs (one-dimensional space-time plots) of a supracellular cable that is cut during the ablation, and manually created tracks of visible features, such as the resulting cut ends. These tracks allow to estimate, for instance, recoil velocities of the cut tissue and may be used to evaluate automated methods for estimating said velocities.</p> <p>This dataset is used in the manuscript to evaluate various variational approaches for joint motion estimation and source identification:</p> <p>L. F. Lang, N. Dutta, E. Scarpa, B. Sanson, C.-B. Schönlieb, and J. Étienne. Joint Motion Estimation and Source Identification using Convective Regularisation with an Application to the Analysis of Laser Nanoablations. 2019.</p> <p><strong>Description</strong></p> <p>The movies depict a square region of approximately <span class="math-tex">\(42.2 \times 42.2 \, \mathrm{\mu m}^{2}\)</span> at a spatial resolution of <span class="math-tex">\(250 \times 250\)</span> pixels. A typical sequence contains between 60 and 100 frames. They temporal interval between recorded frames was <span class="math-tex">\(727.67 \, \mathrm{ms}\)</span>.</p> <p>Each sequence features cell membranes labelled with E-cadherin:GFP and shows a single plasma-induced laser nanoablation. The destructed tissue region is roughly of <span class="math-tex">\(2 \, \mathrm{\mu m}\)</span> length. This ablation is expected to have a width of the order of the size of one pixel. During the ablation the acquisition is paused, resulting in a black image.</p> <p>For the used microscopy techniques and for the preparation of flies, as well as for the details of the laser ablation method, see the paper:</p> <p>E. Scarpa, C. Finet, G. B. Blanchard, and B. Sanson. Actomyosin-driven tension at compartmental boundaries orients cell division independently of cell geometry In Vivo. Dev. Cell, 47(6):727–740.e6, December 2018. URL: <a href="https://doi.org/10.1016/j.devcel.2018.10.029">https://doi.org/10.1016/j.devcel.2018.10.029</a></p> <p>The kymographs and the manually created annotations (tracks) of features were created using Fiji (<a href="https://fiji.sc/">https://fiji.sc/</a>).</p> <p><strong>Content</strong></p> <p>The dataset contains 15 sequences placed in the following folder structure:</p> <ul> <li>SqAX3_SqhGFP42_GAP43_TM6B <ul> <li>190216E4PSB1</li> <li>190216E5PSB1</li> <li>190216E5PSB2</li> <li>190216E6PSB1</li> <li>190216E8PSB1</li> <li>E2PSB1</li> <li>E5PSB2</li> <li>E8PSB1</li> <li>PSB1E1</li> <li>PSB4</li> </ul> </li> <li>SqhGFP40 <ul> <li>e1_PSB8</li> <li>e3_PSB9</li> <li>e3_PSB10</li> <li>e4_PSB11</li> <li>e4_PSB12</li> </ul> </li> </ul> <p>Each folder contains:</p> <ul> <li>The sequence itself in TIF format, e.g. "190216E4PSB1PMT - PMT [560-] _C1.ome.tif".</li> <li>A file "reslice.roi" that indicates the location/direction of the cut supracellular cable.</li> <li>3 different kymographs for each sequence obtained by taking avg/max/sum projections in Fiji orthogonal to the line specified in "reslice.roi", e.g. <ul> <li>"AVG_Reslice of 190216E4PSB1PMT.tif",</li> <li>"MAX_Reslice of 190216E4PSB1PMT.tif",</li> <li>"SUM_Reslice of 190216E4PSB1PMT.tif".</li> </ul> </li> <li>Text files that state the time/space coordinates of manually tracked features in the kymographs, e.g. <ul> <li>"cutend_L.txt" (coordinates of the left cut end after the ablation),</li> <li>"cutend_R.txt" (coordiantes of the right cut end),</li> <li>"feat_X.txt" (coordinates of additional features, where X is a number and L or R).</li> </ul> </li> <li>A ZIP file "manual_ROIs.zip" that contains all the coordinates of tracked features of the kymograph in ROI format (e.g. "cutend_L.roi").</li> </ul> <p><strong>Usage</strong></p> <p>The sequences, kymographs, and the tracks can be viewed using, for example, Fiji.</p> <p>For the automated analysis, see the Python code that accompanies the manuscript above. It is available at https://dx.doi.org/XXX</p> <p><strong>License information</strong></p> <p>This dataset is released under Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. See <a href="https://creativecommons.org/licenses/by-nc-sa/4.0/">CC BY-NA-SC 4.0</a>.</p> <p><strong>How to cite this dataset</strong></p> <p>If you use this dataset in an academic publication, please consider citing the paper:</p> <p>L. F. Lang, N. Dutta, E. Scarpa, B. Sanson, C.-B. Schönlieb, and J. Étienne. Joint Motion Estimation and Source Identification using Convective Regularisation with an Application to the Analysis of Laser Nanoablations. 2019.</p> <p>To cite solely the dataset, please use:</p> <p>L. F. Lang, N. Dutta, E. Scarpa, B. Sanson, C.-B. Schönlieb, and J. Étienne. (2019). Microscopy image sequences and annotated kymographs of laser ablation experiments in Drosophila embryos [Data set]. Zenodo. <a href="https://doi.org/10.5281/zenodo.3257654">http://doi.org/10.5281/zenodo.3257654</a></p>
Training data for 'Genome annotation with Apollo' tutorial (Galaxy Training Material)
<p>Published scaffolds from the Apis mellifera assembly Amel_4.5 and Official Gene Set 3.2.</p> <p>Source: <a href="http://hymenopteragenome.org/beebase/?q=download_sequences">http://hymenopteragenome.org/beebase/?q=download_sequences</a></p>
IBM Watson's NLP model for annotating potato literature.
<p>Archived files(.zip) of the IBM Watson's domain specific supervised NLP model for annotating potato literature. Created with the help of <a href="https://www.ibm.com/watson/services/knowledge-studio/">Watson Knowledge Studio</a> </p>
Peromyscus genome annotation
<p>Genome annotations and predicted proteins and transcripts for Peromyscus attwateri, nudipes, aztecus, melanophrys. </p>
The Caedibacter taeniospiralis genome sequence and annotation
<p>Interest in host-symbiont interactions is continuously increasing, not only due to the relevance and<br> prevalence of microbiomes. Started with the detection and description of novel symbionts, attention<br> moves to the molecular consequences and innovations of symbioses. However, molecular analysis requires<br> genome data which is dicult to obtain from obligate intracellular and uncultivated bacteria.We describe<br> here the Caedibacter taeniospiralis genome and transcriptome, identified by DNA and RNA Dual-Seq<br> of infected paramecia.</p> <p>Data inlcudes a genome FASTA file, annotations of genes and operons in gff format, and the compelte annotation in Geneious format.</p>
Genome annotations of Solanaceae species
<p>This archive contains genome annotations of <em>Solanaceae</em> species (i.e., <em>S. lycopersicum</em>, <em>S. pennellii</em> and <em>S. tuberosum</em>). The annotation files include gene modes and genetic markers from the <a href="https://solgenomics.net/">Sol Genomics Network</a> (SGN) resource that were converted to semantically interoperable format using the <a href="http://10.5281/zenodo.1076437">SIGA.py</a> command-line tool. The data are (re)distributed in:</p> <ul> <li><a href="https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md">Generic Feature Format</a> files (.gff)</li> <li><a href="https://sqlite.org/">SQLite</a> database files (.db)</li> <li><a href="https://www.w3.org/TR/turtle/">RDF/</a><a href="https://www.w3.org/TR/turtle/">Turle</a> files (gzip-ed .ttl)</li> </ul>
Improved genome assembly and annotation of the soybean aphid (Aphis glycines Matsumura)
<p>Updated genome assembly and annotation of <em>Aphis glycines</em> biotype 4.</p> <p><strong>Overview of files included in this release:</strong></p> <p><strong>Frozen release:</strong></p> <p>Updated <em>A. glycines </em>biotype 4 genome assembly: Aphis_glycines_4.v2.1.scaffolds.fa.gz </p> <p>BRAKER2 gene models for updated <em>A. glycines </em>biotype 4 genome assembly: Aphis_glycines_4.v2.1.scaffolds.fa.gff</p> <p>BRAKER2 protein sequences: Aphis_glycines_4.v2.1.scaffolds.fa.gff.aa.fa</p> <p>BRAKER2 nucleotide coding sequences: Aphis_glycines_4.v2.1.scaffolds.fa.gff.CDS.fa</p> <p><strong>Unfiltered raw intermediate genome assemblies:</strong></p> <p>Canu assembly of biotype 4 PacBio data from Wenger et. al. (2017): canu.fa.gz</p> <p>DBG2OLC hybrid assembly of selected biotype 4 MiSeq data and biotype 4 PacBio data from Wenger et. al. (2017): DBG2OLC.fa.gz</p> <p>Merged Canu and DBG2OLC assembly created with quickmerge: quickmerge.fa.gz</p> <p>Pilon polished (2 rounds) quickmerge assembly: quickmerge.pilon_r2.fa.gz</p> <p><strong>Mitochondrial and endosymbiont contigs extracted from the pilon polished quickmerge assembly: </strong></p> <p><em>A. glycines </em>biotype 4 mitochondrial genome: Aphis_glycines_4_Buchnera_v1.fa</p> <p><em>A. glycines </em>biotype 4 <em>Buchnera aphidicola</em> contigs: Aphis_glycines_4_Buchnera_v1.fa</p> <p><em>A. glycines </em>biotype 4 <em>Wolbachia</em> contigs: Aphis_glycines_4_Buchnera_v1.fa</p> <p><strong>Other files:</strong></p> <p>MUSCLE alignment of <em>A. glycines </em>v1, <em>A. glycines </em>biotype 4 v2.1 and <em>Drosophila melanogaster</em> R6.22 Osiris proteins in fasta format: D_mel_v1_v2_osiris.prots.muscle.fasta</p> <p>FastTree Maximum Likelihood phylogeny based on the MUSCLE alignment of Osiris genes in newick format: D_mel_v1_v2_osiris.prots.muscle.FastTree.nwk</p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p>
A Study of Annotation and Alignment Accuracy for Performance Comparison in Complex Orchestral Music
<p>Dataset accompanying the paper published at ISMIR 2019.</p> <p>See included README file for details.</p>
HIV-1 genome and annotation
<p>HIV-1 genome and annotation datasets for use with Galaxy Training Materials (<a href="https://training.galaxyproject.org/">https://training.galaxyproject.org</a>). This repository contains three datasets:</p> <ol> <li>hbx2.fa - genomic sequence of HIV-1 derived from GenBank entry K03455.1 </li> <li>hxb2.bed - coordinates of genomic features and drug resistance mutations </li> <li>hxb2.dr.bed - a subset of the annotation data containing drug resistance mutations only.</li> </ol> <p>Coordinates of drug resistance mutations are derived from Los Alamos National Lab HIV <a href="https://www.hiv.lanl.gov/content/sequence/HIV/MAP/hxb2.xls">database data</a>.</p>
Figs. 6 a-f in Pluteus section Celluloderma (Pluteaceae, Agaricales) in Brazil: additional morphological studies and an annotated checklist of all named taxa
Figs. 6 a-f. Pluteus rimosoaffinis (A.M. Gugliotta et al. PEFI07/2009). a. Basidiomata; b. Basidiospores; c. Basidia; d. Pleurocystidia; e. Cheilocystidia; f. Pileipellis elements. Bars: a = 1 cm; b–f = 10 µm.
Figs. 4 a-d in Pluteus section Celluloderma (Pluteaceae, Agaricales) in Brazil: additional morphological studies and an annotated checklist of all named taxa
Figs. 4 a-d. Pluteus cf. fuliginosus (FK2158). a. Basidiospores; b. Pleurocystidia; c. Cheilocystidia; d. Pileipellis elements. Bars = 10 µm.
Figs. 2 a-d in Pluteus section Celluloderma (Pluteaceae, Agaricales) in Brazil: additional morphological studies and an annotated checklist of all named taxa
Figs. 2 a-d. Pluteus diptychocystis (NMJ184). a. Basidiospores; b. Pleurocystidia; c. Cheilocystidia; d. Pileipellis elements. Bars = 10 µm.
Text-fig. 2. A – Elasmobranchii gen. et spec. indet. specimen NM Pc 02876b; B – Scopeloides glarisianus dentary NM Pc 02888 (the white arrows mark the tips of the "fang-like" teeth); C – S. glarisianus disarticulated skeleton NM Pc 02887a; D – Sardinella sardinites scale NM Pc 02886; E – Clupeidae gen. et spec. indet. articulated skeleton without head NM Pc 02889; F – Anenchelum glarisianum body fragment NM Pc 02880a; G – Percoidei gen. et sp. indet. preoperculum (G-1) and its interpretation (G-2) NM Pc 02891. The arrow shows the enlarged spine in the angle between rami verticalis and horizontalis. Abbreviations: cl – cleithrum; op – operculum; pcl – postcleithrum. in An Annotated List Of The Oligocene Fish Fauna From The Osíčko Locality (Menilitic Fm.; Moravia, The Czech Republic)
Text-fig. 2. A – Elasmobranchii gen. et spec. indet. specimen NM Pc 02876b; B – Scopeloides glarisianus dentary NM Pc 02888 (the white arrows mark the tips of the "fang-like" teeth); C – S. glarisianus disarticulated skeleton NM Pc 02887a; D – Sardinella sardinites scale NM Pc 02886; E – Clupeidae gen. et spec. indet. articulated skeleton without head NM Pc 02889; F – Anenchelum glarisianum body fragment NM Pc 02880a; G – Percoidei gen. et sp. indet. preoperculum (G-1) and its interpretation (G-2) NM Pc 02891. The arrow shows the enlarged spine in the angle between rami verticalis and horizontalis. Abbreviations: cl – cleithrum; op – operculum; pcl – postcleithrum.
Text-fig. 3. "Glossanodon" musceli A – nearly complete specimen NM Pc 02875a; B – caudal skeleton of specimens NM Pc 02871b and NM Pc 02871a (B-1 and B-2 respectively; part and counterpart) and its tentative reconstruction (B-3); C – specimen NM Pc 02873a, general view (C-1) and detail of the head (C-2); D – specimen NM Pc 02874a (the white arrow shows normally developed neural spine on the anterior abdominal vertebra). Abbreviations: ao – antorbitale; d – dentale; epu – epurale; fr – frontale; hp1-6 – hypurals 1-6; io – infraorbitals; mx – maxillare; npu2 – neural spine of second preural vertebra; ph – parhypurale; pu1 – first preural vertebra; pop – preoperculum; psp – parasphenoideum; stu – stegurale; u1 – urale 1; u2 – urale 2. in An Annotated List Of The Oligocene Fish Fauna From The Osíčko Locality (Menilitic Fm.; Moravia, The Czech Republic)
Text-fig. 3. "Glossanodon" musceli A – nearly complete specimen NM Pc 02875a; B – caudal skeleton of specimens NM Pc 02871b and NM Pc 02871a (B-1 and B-2 respectively; part and counterpart) and its tentative reconstruction (B-3); C – specimen NM Pc 02873a, general view (C-1) and detail of the head (C-2); D – specimen NM Pc 02874a (the white arrow shows normally developed neural spine on the anterior abdominal vertebra). Abbreviations: ao – antorbitale; d – dentale; epu – epurale; fr – frontale; hp1-6 – hypurals 1-6; io – infraorbitals; mx – maxillare; npu2 – neural spine of second preural vertebra; ph – parhypurale; pu1 – first preural vertebra; pop – preoperculum; psp – parasphenoideum; stu – stegurale; u1 – urale 1; u2 – urale 2.
Fig. 53 in Revisional notes on the genus Microhoria Chevrolat, 1877 (Insecta: Coleoptera: Anthicidae) from the Eastern Mediterranean and Turkey, with new descriptions, an annotated catalogue, and a key
Fig. 53. Microhoria walkeri sp. nov. A – Male holotype, habitus, dorsal view; B – ditto, forebody, dorsal view; C – Male paratype, spiculum gastrale; D – ditto, aedeagus, lateral view [not to scale].
ScienceDex guides
Understand access before you commit
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.