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Figure 1 from: Mounce R, Murray-Rust P, Wills M (2017) A machine-compiled microbial supertree from figure-mining thousands of papers. Research Ideas and Outcomes 3: e13589. https://doi.org/10.3897/rio.3.e13589
Figure 1 - Overall workflow; from content acquisition to stripping figure images out of the PDF, to image filtering, image analysis and reconversion back into re-usable, machine-readable phylogenetic data.
Figure 4 from: Mounce R, Murray-Rust P, Wills M (2017) A machine-compiled microbial supertree from figure-mining thousands of papers. Research Ideas and Outcomes 3: e13589. https://doi.org/10.3897/rio.3.e13589
Figure 4 - Output from image analysis of the input tree image in figure 1. All taxa and relationships are correctly reproduced, with branch lengths also preserved with high fidelity. (Note that the vertical ordering of the tips is not meaningful and is arbitrarily created by the display software.)
Figure 5 from: Mounce R, Murray-Rust P, Wills M (2017) A machine-compiled microbial supertree from figure-mining thousands of papers. Research Ideas and Outcomes 3: e13589. https://doi.org/10.3897/rio.3.e13589
Figure 5 - Screenshot of exemplar machine-readable NeXML formatted data output from our automated analysis of the figure image from figure 1 of Park et al. 2008. Note that the genus, species, strain, and Genbank Accession numbers are semantically distinguished where detected. Heuristic post-OCR autocorrection processes are also noted where these have been applied (e.g. the conversion of a letter 'Z' to the number '2' in many Genbank Accession numbers). A machine-readable version of this file is supplied as supplementary material (Suppl. material 2).
Figure 3 from: Mounce R, Murray-Rust P, Wills M (2017) A machine-compiled microbial supertree from figure-mining thousands of papers. Research Ideas and Outcomes 3: e13589. https://doi.org/10.3897/rio.3.e13589
Figure 3 - Number of leaves (terminal taxa) in each of 1614 source tree images (blue) and number of leaves recovered-from each image (orange). The modal number of taxa recovered per image was 12, the median was 13, and the mean was 13.96. The modal number of taxa not recovered from the trees was 2, the median was 5 and the mean was 7.15. The image mining process is lossy since most output tree files did not recover all of the taxa from the source image.
Figure 2 from: Mounce R, Murray-Rust P, Wills M (2017) A machine-compiled microbial supertree from figure-mining thousands of papers. Research Ideas and Outcomes 3: e13589. https://doi.org/10.3897/rio.3.e13589
Figure 2 - A typical source input tree raster image (figure 1 from Park et al. 2008). Note the low resolution image quality. As this computer-generated ilustration follows predefined rules and conventions for the visual display of phylogenetic trees, we do not believe that it qualifies as a copyrightable work in itself (see Egloff et al. 2017 for more).
Figure 6 from: Jahn R, Kusber W-H, Cocquyt C (2017) Differentiating Iconella from Surirella (Bacillariophyceae): typifying four Ehrenberg names and a preliminary checklist of the African taxa. PhytoKeys 82: 73-112. https://doi.org/10.3897/phytokeys.82.13542
Figure 6 - Iconella tchadensis. A–D Valves from the holotype slide BR 987 A–C valvar views showing the size range D girdle view. Scale bar = 10 µm.
Figure 7 from: Mounce R, Murray-Rust P, Wills M (2017) A machine-compiled microbial supertree from figure-mining thousands of papers. Research Ideas and Outcomes 3: e13589. https://doi.org/10.3897/rio.3.e13589
Figure 7 - Comparison between our supertree (left) and the NCBI Taxonomy reference tree (right): This example section of the supertree corresponds to taxa mostly from Rhodospirillaceae with the exception of rogue taxa indicated with a red asterisk. This section is related to the NCBI taxonomy reference tree on the right, containing those Rhodospirillaceae species leaves included in the supertree analysis (27). Nine taxa out of the 27 Rhodospirillaceae included were reconstructed elsewhere in our supertree (not shown). This is representative of the phylogenetic placement errors found throughout the supertree: individual rogue taxa, as well as misplaced clades of related taxa.
Figure 8 from: Mounce R, Murray-Rust P, Wills M (2017) A machine-compiled microbial supertree from figure-mining thousands of papers. Research Ideas and Outcomes 3: e13589. https://doi.org/10.3897/rio.3.e13589
Figure 8 - A visual exploration of taxon overlap of the 924 source trees used in this supertree analysis using the Supertree Toolkit 2 (Hill and Davis 2014). This demonstrates that there is not connectivity between all of the source trees we used in our supertree analysis.
Figure 4 from: Jahn R, Kusber W-H, Cocquyt C (2017) Differentiating Iconella from Surirella (Bacillariophyceae): typifying four Ehrenberg names and a preliminary checklist of the African taxa. PhytoKeys 82: 73-112. https://doi.org/10.3897/phytokeys.82.13542
Figure 4 - Surirella undulata. A–C Drawing BHUPM 1163 D Lectotype: BHUPM 540138-6, Trockenpräparate CXXXVIII 6. Scale bar for D = 10 µm.
Figure 5 from: Jahn R, Kusber W-H, Cocquyt C (2017) Differentiating Iconella from Surirella (Bacillariophyceae): typifying four Ehrenberg names and a preliminary checklist of the African taxa. PhytoKeys 82: 73-112. https://doi.org/10.3897/phytokeys.82.13542
Figure 5 - Iconella murielae. Valve from the holotype slide BR 984. A, C Overview of the entire valve at different foci B, D Detail of the middle part of the valve at different foci B is showing the fenestral openings below the raphe canal and D the striae and the transapical undulations. Scale bar for A, C = 20 µm; scale bar for B, D = 10 µm.
Figure 2 from: Jahn R, Kusber W-H, Cocquyt C (2017) Differentiating Iconella from Surirella (Bacillariophyceae): typifying four Ehrenberg names and a preliminary checklist of the African taxa. PhytoKeys 82: 73-112. https://doi.org/10.3897/phytokeys.82.13542
Figure 2 - Iconella splendida. Lectotype: Drawing BHUPM 1160. A The alive cell representing the lectotype in three views (hand written numbers 2-4), length 188 µm B Later documentation of valve details by Ehrenberg, hand written numbers 5-6 represent a 226 µm long cell.
Figure 3 from: Jahn R, Kusber W-H, Cocquyt C (2017) Differentiating Iconella from Surirella (Bacillariophyceae): typifying four Ehrenberg names and a preliminary checklist of the African taxa. PhytoKeys 82: 73-112. https://doi.org/10.3897/phytokeys.82.13542
Figure 3 - Surirella librile. Lectotype: Drawing BHUPM 1151. A Girdle view representing the lectotype (corresponding to preparation BHUPM 540177-3 in 3D) B Valvar view representing the lectotype; Ehrenberg indicated two views of one cell with dots between the undulated girdle view in A and the valvar view in B. C Corresponding preparation BHUPM 540177-4 D Corresponding preparation BHUPM 540177-3 E Documentation of Ehrenberg's observations in 1826 F Small cells in girdle view not correponding to the published protologue. Scale bar for C–D = 10 µm.
Figures 14-20 from: Liu S-N, Tang L, Luo R-T (2017) Notes on the Stenus cirrus group of Zhejiang, East China, with descriptions of two new species (Coleoptera, Staphylinidae). ZooKeys 684: 75-84. https://doi.org/10.3897/zookeys.684.13514
Figures 14-20 Stenus yuyimingi. 14 male sternite VII 15 male sternite VIII 16 male sternite IX 17, 18 aedeagus 19 female sternite VIII 20 valvifers and spermatheca. Scale bars: 0.25 mm.
Figures 21-24 from: Liu S-N, Tang L, Luo R-T (2017) Notes on the Stenus cirrus group of Zhejiang, East China, with descriptions of two new species (Coleoptera, Staphylinidae). ZooKeys 684: 75-84. https://doi.org/10.3897/zookeys.684.13514
Figures 21-24 Stenus ovalis. 21 male sternite VIII 22 male sternite IX 23, 24 aedeagus. Scale bars: 0.25 mm.
Figures 7-13 from: Liu S-N, Tang L, Luo R-T (2017) Notes on the Stenus cirrus group of Zhejiang, East China, with descriptions of two new species (Coleoptera, Staphylinidae). ZooKeys 684: 75-84. https://doi.org/10.3897/zookeys.684.13514
Figures 7-13 Stenus wuyanlingus. 7 male sternite VII 8 male sternite VIII 9 male sternite IX 10, 11 aedeagus 12 female sternite VIII 13 valvifers and spermatheca. Scale bars: 0.25 mm.
Figure 1 from: Jahn R, Kusber W-H, Cocquyt C (2017) Differentiating Iconella from Surirella (Bacillariophyceae): typifying four Ehrenberg names and a preliminary checklist of the African taxa. PhytoKeys 82: 73-112. https://doi.org/10.3897/phytokeys.82.13542
Figure 1 - Iconella bifrons A–B Lectotype: BHUPM 540128-6 C–D Ehrenberg's drawing BHUPM 1130 showing different shapes of the same species in Ehrenberg's concept. Scale bar for A = 10 µm.
Figures 1-6 from: Liu S-N, Tang L, Luo R-T (2017) Notes on the Stenus cirrus group of Zhejiang, East China, with descriptions of two new species (Coleoptera, Staphylinidae). ZooKeys 684: 75-84. https://doi.org/10.3897/zookeys.684.13514
Figures 1-6 Habitus. 1, 2Stenus wuyanlingus sp. n. 3, 4Stenus yuyimingi sp. n. 5, 6Stenus ovalis. Scale bars: 1 mm.
Figure 5 from: Hershler R, Liu H-P, Hubbart N (2017) Two new species of Fluminicola (Caenogastropoda, Lithoglyphidae) from southwest Oregon, USA, and a range extension for F. multifarius. ZooKeys 679: 1-20. https://doi.org/10.3897/zookeys.679.13472
Figure 5 - Shells, opercula and radula, F. fresti, sp. n. A Holotype, USNM 1144376 B, C Sympatric ovate-conic and trochiform shell morphs, respectively, USNM 1297149 D Shell, USNM 1297155 E, F Opercula (outer, inner sides), USNM 1422223 G Portion of radular ribbon, USNM 1422223 H Central teeth, USNM 1422223 I Lateral teeth, USNM 1422223. Scale bars: A–D 1.0 mm; E–F 250 µm; G 100 µm; H–I 20 µm.
Figure 4 from: Hershler R, Liu H-P, Hubbart N (2017) Two new species of Fluminicola (Caenogastropoda, Lithoglyphidae) from southwest Oregon, USA, and a range extension for F. multifarius. ZooKeys 679: 1-20. https://doi.org/10.3897/zookeys.679.13472
Figure 4 - Reproductive anatomy. A–D F. multifarius A, B, D USNM 1144567, C USNM 1070753 E–G F. fresti, sp.n., USNM 1422223 H–J F. umpquaensis, sp. n., USNM 1144736. A, E, G Female glandular oviduct and associated structures (viewed from left side) B, C, F, I Bursa copulatrix and seminal receptacle, D, G, J Penis, dorsal surface. The bursa copulatrix and seminal receptacle of type material of F. multifarius (C), which was not illustrated by Hershler et al. (2007), is shown for comparative purposes. Scale bars, 500 µm. Ag albumen gland Bu bursa copulatrix Cg capsule gland Cov coiled oviduct Dsr seminal receptacle duct Ga genital aperture Pd penial duct Pw posterior wall of pallial cavity Sr seminal receptacle Vc ventral channel of capsule gland.
Figure 3 from: Hershler R, Liu H-P, Hubbart N (2017) Two new species of Fluminicola (Caenogastropoda, Lithoglyphidae) from southwest Oregon, USA, and a range extension for F. multifarius. ZooKeys 679: 1-20. https://doi.org/10.3897/zookeys.679.13472
Figure 3 - Shells, opercula and radula, F. multifarius. A Shell, USNM 1144567 B Shell, USNM 1144997 C Shell, USNM 1145051 D, E Opercula (outer, inner sides), USNM 1144567 F Portion of radular ribbon, USNM 1144567 G Central teeth, USNM 1144567 H Lateral teeth, USNM 1144567. Scale bars: A–B 1.0 mm; D–E 250 µm; F, 100 µm; G–H 10 µm.
ScienceDex guides
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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.