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Fig. 10 in A new species of Copionodon representing a relictual occurrence of the Copionodontinae (Siluriformes: Trichomycteridae), with a CT-scan imaging survey of key subfamilial features

Fig. 10. Copionodon exotatos, holotype, MZUSP 120631, CT-scan images of right premaxilla and associated dentition: a. ventral view, b. dorsal view.

Fig. 6 in A new species of Copionodon representing a relictual occurrence of the Copionodontinae (Siluriformes: Trichomycteridae), with a CT-scan imaging survey of key subfamilial features

Fig. 6. Copionodon exotatos, paratype, MZUSP 121656. Lower jaw, left side, mesial view. Abbreviations: AA, anguloarticular; DEN, dentary. Scale bar = 1 mm.

Fig. 1 in A new species of Copionodon representing a relictual occurrence of the Copionodontinae (Siluriformes: Trichomycteridae), with a CT-scan imaging survey of key subfamilial features

Fig. 1. Copionodon exotatos, holotype, MZUSP 120631, 45.0 mm SL, Brazil, Bahia, Chapada Diamantina, Município de Palmeiras, Riacho do Mosquito, immediately upstream from Cachoeira do Mosquito, rio Paraguaçu basin.

Fig. 2 in A new species of Copionodon representing a relictual occurrence of the Copionodontinae (Siluriformes: Trichomycteridae), with a CT-scan imaging survey of key subfamilial features

Fig. 2. Copionodon exotatos, holotype, MZUSP 120631, 45.0 mm SL. Left to right, dorsal and ventral views of head.

opencc-by-4.0Apr 2020View details →

A five-tile tomographic micro-CT dataset of the oak sculpture "Holy woman with lantern" - part 2 of 2

Summary This submission contains a five-tile tomographic datasets of an oak sculpture Holy woman with lantern, belonging to the Rijksmuseum collection. The first part consists of the first three tiles, the second part of the last two tiles. The data is made available as part of [Bossema et al., 2020] and [Domínguez-Delmás et al., 2020].   Apparatus The dataset is acquired using the custom-built and highly flexible CT scanner, FleX-ray Laboratory, developed by TESCAN-XRE, located at CWI in Amsterdam. This apparatus consists of a cone-beam microfocus X-ray point source that projects polychromatic X-rays onto a 1944-by-1536 pixels, 14-bit, flat detector panel. Full details can be found in [Coban 2020]. Sample Information The sample is an oak sculpture of a Holy woman with lantern, 35.8 cm high, c. 1500-1525 [Rijksmuseum inventory number BK-NM-9253,  https://www.rijksmuseum.nl/en/collection/BK-NM-9253]. It was mounted on a wooden block on the rotation stage. See Figure 7 in [Bossema et al., 2020] for a picture of the object and the mount and [Domínguez-Delmás, 2020] for analysis of the reconstructed images.     Experimental Plan The data in this submission was collected to facilitate measurements of the tree rings (dendrochronological research) at different heights, and to illustrate the use of detector tiling for the investigation cultural heritage objects. To image the entire object, five vertical tiles were scanned at image resolution 67.8 micron. For each scan, the sample was rotated 360° in circular and continuous motion, with a dark-field (closed-shutter), and 2 flat-field (open-shutter) images taken before and after the acquisition. The datasets of Tile 1-4 consist of 2914 projections, the dataset of Tile 5 of 1500 projections. All raw data (i.e. no corrections) is made available in .tif format. List of Contents The content of the submission is given below. part 1: <ul> <li>t1: first vertical tile, bottom of sculpture</li> <li>t2: second vertical tile</li> <li>t3: third vertical tile</li> </ul> part 2: <ul> <li>t4: fourth vertical tile</li> <li>t5: fifth vertical tile, top of the sculpture</li> </ul> Each data folder contains: <ul> <li>dark-field (or closed-shutter) image, di000000.tif,</li> <li>flat-field (or open-shutter) image before acquisition, io000000.tif, and after acquisition, io000001.tif,</li> <li>raw (unprocessed or uncorrected) projections, scan_*.tif,</li> <li>data settings XRE.txt, a text file with scanner metadata,</li> <li>scan settings.txt, a text file with scanner metadata in more human readable format, and</li> <li>data settings XRE.ini, a snapshot text file of basic geometry information at the start of a scan.</li> <li>script_executed.txt, the text file containing the list of commands the apparatus has executed.</li> </ul> Additional Links These datasets are produced by the <a href="https://www.cwi.nl/research/groups/computational-imaging">Computational Imaging group</a> at Centrum Wiskunde & Informatica (CI-CWI). For any relevant Python/MATLAB scripts for the FleX-ray datasets, we refer the reader to our group's <a href="http://github.com/cicwi">GitHub page</a>. Contact Details For more information or guidance in using these datasets, please get in touch with  <ul> <li>bossema [at] cwi.nl</li> </ul> Acknowledgments We thank Paul van Duin and Marta Domínguez Delmás for providing us with the opportunity to scan this interesting object.

opencc-by-4.0Apr 2020View details →

A five-tile tomographic micro-CT dataset of the oak sculpture "Holy woman with lantern" - part 1 of 2

Summary This submission contains a five-tile tomographic datasets of an oak sculpture Holy woman with lantern, belonging to the Rijksmuseum collection. The first part consists of the first three tiles, the second part of the last two tiles. The data is made available as part of [Bossema et al., 2020] and [Domínguez-Delmás et al., 2020].   Apparatus The dataset is acquired using the custom-built and highly flexible CT scanner, FleX-ray Laboratory, developed by TESCAN-XRE, located at CWI in Amsterdam. This apparatus consists of a cone-beam microfocus X-ray point source that projects polychromatic X-rays onto a 1944-by-1536 pixels, 14-bit, flat detector panel. Full details can be found in [Coban 2020]. Sample Information The sample is an oak sculpture of a Holy woman with lantern, 35.8 cm high, c. 1500-1525 [Rijksmuseum inventory number BK-NM-9253,  https://www.rijksmuseum.nl/en/collection/BK-NM-9253]. It was mounted on a wooden block on the rotation stage. See Figure 7 in [Bossema et al., 2020] for a picture of the object and the mount and [Domínguez-Delmás, 2020] for analysis of the reconstructed images.     Experimental Plan The data in this submission was collected to facilitate measurements of the tree rings (dendrochronological research) at different heights, and to illustrate the use of detector tiling for the investigation cultural heritage objects. To image the entire object, five vertical tiles were scanned at image resolution 67.8 micron. For each scan, the sample was rotated 360° in circular and continuous motion, with a dark-field (closed-shutter), and 2 flat-field (open-shutter) images taken before and after the acquisition. The datasets of Tile 1-4 consist of 2914 projections, the dataset of Tile 5 of 1500 projections. All raw data (i.e. no corrections) is made available in .tif format. List of Contents The content of the submission is given below. part 1: <ul> <li>t1: first vertical tile, bottom of sculpture</li> <li>t2: second vertical tile</li> <li>t3: third vertical tile</li> </ul> part 2: <ul> <li>t4: fourth vertical tile</li> <li>t5: fifth vertical tile, top of the sculpture</li> </ul> Each data folder contains: <ul> <li>dark-field (or closed-shutter) image, di000000.tif,</li> <li>flat-field (or open-shutter) image before acquisition, io000000.tif, and after acquisition, io000001.tif,</li> <li>raw (unprocessed or uncorrected) projections, scan_*.tif,</li> <li>data settings XRE.txt, a text file with scanner metadata,</li> <li>scan settings.txt, a text file with scanner metadata in more human readable format, and</li> <li>data settings XRE.ini, a snapshot text file of basic geometry information at the start of a scan.</li> <li>script_executed.txt, the text file containing the list of commands the apparatus has executed.</li> </ul> Additional Links These datasets are produced by the <a href="https://www.cwi.nl/research/groups/computational-imaging">Computational Imaging group</a> at Centrum Wiskunde & Informatica (CI-CWI). For any relevant Python/MATLAB scripts for the FleX-ray datasets, we refer the reader to our group's <a href="http://github.com/cicwi">GitHub page</a>. Contact Details For more information or guidance in using these datasets, please get in touch with  <ul> <li>bossema [at] cwi.nl</li> </ul>   Acknowledgments We thank Paul van Duin and Marta Domínguez Delmás for providing us with the opportunity to scan this interesting object.

Figure 4 from: Bernardes M, Le MD, Nguyen TQ, Pham CT, Pham AV, Nguyen TT, Rödder D, Bonkowski M, Ziegler T (2020) Integrative taxonomy reveals three new taxa within the Tylototriton asperrimus complex (Caudata, Salamandridae) from Vietnam. ZooKeys 935: 121-164. https://doi.org/10.3897/zookeys.935.37138

Figure 4 Phylogram based on the Bayesian analysis. Number above and below branches are MP/ML bootstrap values and Bayesian posterior probabilities (> 50 %), respectively. Dashes represent values < 50 %. Sample AB769531 is from Nishikawa et al. 2013b.

Figure 5 from: Bernardes M, Le MD, Nguyen TQ, Pham CT, Pham AV, Nguyen TT, Rödder D, Bonkowski M, Ziegler T (2020) Integrative taxonomy reveals three new taxa within the Tylototriton asperrimus complex (Caudata, Salamandridae) from Vietnam. ZooKeys 935: 121-164. https://doi.org/10.3897/zookeys.935.37138

Figure 5 Scatterplot between PC1 and PC2 of the morphological characters corrected to SVL and log–transformed, for A taxon 1 and taxon 2 of the Vietnamese Tylototriton cf. asperrimusB the head- and dorso- related data of taxon 3 from Lai Chau Province and T. cf. asperrimus from Vietnam sensu lato; and C the limb related data of taxon 3 from Lai Chau Province and T. cf. asperrimus from Vietnam sensu lato. In the graphics T. cf. refers to T. cf. asperrimus.

Figure 3 from: Bernardes M, Le MD, Nguyen TQ, Pham CT, Pham AV, Nguyen TT, Rödder D, Bonkowski M, Ziegler T (2020) Integrative taxonomy reveals three new taxa within the Tylototriton asperrimus complex (Caudata, Salamandridae) from Vietnam. ZooKeys 935: 121-164. https://doi.org/10.3897/zookeys.935.37138

Figure 3 Holotype of Tylototriton asperrimus (ZMB 34089). In sequence: dorsal view; ventral view; lateral view with detail of ovaries; and detail of dorsal view of the head. Photographs T. Ziegler.

Figure 2 from: Bernardes M, Le MD, Nguyen TQ, Pham CT, Pham AV, Nguyen TT, Rödder D, Bonkowski M, Ziegler T (2020) Integrative taxonomy reveals three new taxa within the Tylototriton asperrimus complex (Caudata, Salamandridae) from Vietnam. ZooKeys 935: 121-164. https://doi.org/10.3897/zookeys.935.37138

Figure 2 Distribution map of the new populations of Tylototriton from North Vietnam, based on the following symbols: square (taxon 3, this study) the population from Sin Ho District, Lai Chau Province; diamond (taxon 1, this study) the upper one identifies the population from Van Ho District, Son La Province, and the lower one identifies the population from Thuong Xuan District, Thanh Hoa Province; triangle (taxon 2, this study) the upper one identifies the population from Tan Son District, Phu Tho Province, the middle one identifies the population from Da Bac District, Hoa Binh Province, and the lower one identifies the population from Lac Son District, Hoa Binh Province. The two populations identified by the circles represent T. asperrimus sensu stricto from China. High resolution remote sensing land cover information was extracted from "GLAD-UMD and SERVIR-Mekong, Natural annual tree canopy structure and surface water dynamics products, 2017" (lower left panel). Bioclimatic variables (right side) were extracted from remote sensing data provided by Deblauwe et al. (2016).

Figure 7 from: Bernardes M, Le MD, Nguyen TQ, Pham CT, Pham AV, Nguyen TT, Rödder D, Bonkowski M, Ziegler T (2020) Integrative taxonomy reveals three new taxa within the Tylototriton asperrimus complex (Caudata, Salamandridae) from Vietnam. ZooKeys 935: 121-164. https://doi.org/10.3897/zookeys.935.37138

Figure 7 Boxplot of the most differing characters related to limb values between taxon 1, taxon 2, and taxon 3. Characters were corrected to SVL and log–transformed. For abbreviations see Materials and methods.

Figure 10 from: Bernardes M, Le MD, Nguyen TQ, Pham CT, Pham AV, Nguyen TT, Rödder D, Bonkowski M, Ziegler T (2020) Integrative taxonomy reveals three new taxa within the Tylototriton asperrimus complex (Caudata, Salamandridae) from Vietnam. ZooKeys 935: 121-164. https://doi.org/10.3897/zookeys.935.37138

Figure 10 Tylototriton pasmansi obsti ssp. nov. (holotype) In sequence: dorsal view; ventral view; lateral view; and detail of dorsal view of the head. Photographs T. Ziegler.

Figure 1 from: Bernardes M, Le MD, Nguyen TQ, Pham CT, Pham AV, Nguyen TT, Rödder D, Bonkowski M, Ziegler T (2020) Integrative taxonomy reveals three new taxa within the Tylototriton asperrimus complex (Caudata, Salamandridae) from Vietnam. ZooKeys 935: 121-164. https://doi.org/10.3897/zookeys.935.37138

Figure 1 Current distribution map of the genus Tylototriton, from South and Central China, to northern Vietnam, Laos, Thailand, Myanmar, India, Bhutan and Nepal (Hernandez 2016; Qian et al. 2017; Grismer et al. 2018; Wang et al. 2018; Grismer et al. 2019; Hernandez et al. 2019; Zaw et al. 2019). In red the distribution areas belonging to the subgenus Tylototriton, and in blue the distribution areas belonging to the sub–genus Yaotriton (Dubois and Raffaëlli 2009). The numerical identification corresponds to the different species and undescribed taxa as follow: 1T. himalayanus2T. cf. himalayanus (Bhutan) 3T. cf. verrucosus (Manipur) 4T. kachinorum5T. verrucosus6T. ngarsuensis7T. shanorum8T. shanjing9T. pseudoverrucosus10T. taliangensis11T. kweichowensis12T. yangi13T. pulcherrimus14T. anguliceps15T. uyenoi16T. podichthys17T. panhai18T. notialis19Tylototriton taxon 2, this study 20Tylototriton taxon 3, this study 21T. ziegleri22T. vietnamensis23T. hainanensis24T. cf. hainanensis (Baise) 25T. cf. wenxianensis (Libo) 26T. cf. wenxianensis (Guizhou) 27T. asperrimus28T. cf. asperrimus (Guangdong) 29T. lizhengchangi30T. liuyangensis31T. broadoridgus32T. cf. wenxianensis (Chongquing and Hubei) 33T. wenxianensis34T. dabienicus35T. anhuiensis and 36T. panwaensis.

Figure 9 from: Bernardes M, Le MD, Nguyen TQ, Pham CT, Pham AV, Nguyen TT, Rödder D, Bonkowski M, Ziegler T (2020) Integrative taxonomy reveals three new taxa within the Tylototriton asperrimus complex (Caudata, Salamandridae) from Vietnam. ZooKeys 935: 121-164. https://doi.org/10.3897/zookeys.935.37138

Figure 9 Dorsal and ventral views of the new taxa in life. Top: Tylototriton pasmansi sp. nov. (holotype); Center: Tylototriton pasmansi obsti ssp. nov. (holotype); Bottom: Tylototriton sparreboomi sp. nov. Photographs: C. T. Pham (upper row) and A. V. Pham (central and lower rows).

Figure 11 from: Bernardes M, Le MD, Nguyen TQ, Pham CT, Pham AV, Nguyen TT, Rödder D, Bonkowski M, Ziegler T (2020) Integrative taxonomy reveals three new taxa within the Tylototriton asperrimus complex (Caudata, Salamandridae) from Vietnam. ZooKeys 935: 121-164. https://doi.org/10.3897/zookeys.935.37138

Figure 11 Tylototriton sparreboomi sp. nov. (holotype). In sequence: dorsal view; ventral view; lateral view; and detail of dorsal view of the head. Photographs T. Ziegler.

Figure 6 from: Bernardes M, Le MD, Nguyen TQ, Pham CT, Pham AV, Nguyen TT, Rödder D, Bonkowski M, Ziegler T (2020) Integrative taxonomy reveals three new taxa within the Tylototriton asperrimus complex (Caudata, Salamandridae) from Vietnam. ZooKeys 935: 121-164. https://doi.org/10.3897/zookeys.935.37138

Figure 6 Boxplot of the most differing characters related to head and dorsal values between taxon 1, taxon 2, and taxon 3. Characters were corrected to SVL and log–transformed. For abbreviations see Materials and methods.

Figure 8 from: Bernardes M, Le MD, Nguyen TQ, Pham CT, Pham AV, Nguyen TT, Rödder D, Bonkowski M, Ziegler T (2020) Integrative taxonomy reveals three new taxa within the Tylototriton asperrimus complex (Caudata, Salamandridae) from Vietnam. ZooKeys 935: 121-164. https://doi.org/10.3897/zookeys.935.37138

Figure 8 Tylototriton pasmansi sp. nov. (holotype). In sequence: dorsal view; ventral view; lateral view; and detail of dorsal view of the head. Photographs T. Ziegler.

opencc-by-4.0Jul 2020View details →

CT image of the upper lumbar and lower thoracic spine

Extract of a computer tomographic imaging dataset of the thorax, showing the upper lumbar and lower thoracic spine, stored as <a href="https://lorensen.github.io/VTKExamples/site/VTKFileFormats/#imagedata">VTK image</a>. The dataset is used to develop the SODALITE virtual clinical trial use-case. It contains a part of the lumbar spine. Starting caudal at L2 which is only partially contained and ending cranial with T9 which also only partially contained. The datasets content is illustrated by the attached png image which shows a volume rendering of the dataset. <pre><code>Format : VTKFile, type="ImageData", version="1.0" Header : ASCII Byte Order : LittleEndian Grid Type : Rectilinear Extend [x,y,z] : 201 , 301 , 161 Spacing [x,y,z] : 0.78125 , 0.78125 , 1.0 Data-Type : Float64 Min Value : 0 Max Value : 2210.5396825 </code></pre>

opencc-zeroAug 2020View details →

Supplementary material 2 from: Shivambu N, Shivambu TC, Downs CT (2020) Assessing the potential impacts of non-native small mammals in the South African pet trade. NeoBiota 60: 1-18. https://doi.org/10.3897/neobiota.60.52871

Table S2