Find research datasets worth reusing

opencc-by-4.0Dec 2020View details →

FIGURE 4 in NSB (Neptune Sandbox Berlin): An expanded and improved database of marine planktonic microfossil data and deep-sea stratigraphy

FIGURE 4. Result page for microfossil occurrences (the specific query here was for radiolarians from samples between 20 and 25 Ma).

opencc-by-4.0Oct 2017View details →

Figure 1 in Ostracods in the plankton of the Sivash Bay (the Sea of Azov) during its transformation from brackish to hypersaline state

Figure 1. Bay Sivash. Occurrence of the five ostracod species (only "alive" specimens) at the sampling stations in 2004, 2014 and 2015. Red icons – Cyprideis torosa, green – Loxoconcha bulgarica, violet – Loxoconcha aestuarii, blue – Cytherois cepa, yellow – Leptocythere devexa.

opencc-by-4.0Oct 2018View details →

Figure 2 in The connection of the intensity of the plankton community luminescence and the age distribution of horse mackerel in the coastal waters of the south-western Crimea

Figure 2. The average monthly intensity of glow organisms 1 – in the winter (January-February); 2 – in the spring (May); 3 — in the summer (June-July) in the 2010-2015.

opencc-by-4.0Oct 2018View details →

Figure 3 in The connection of the intensity of the plankton community luminescence and the age distribution of horse mackerel in the coastal waters of the south-western Crimea

Figure 3. Relative quantity of the age groups the Trachurus mediterraneus (1-yearlings. 2 - two-year-olds. 3 - threeyear-olds. 4 - four-year-olds. 5 - five-year-olds) in the spring-summer period in the coastal waters of the south-western Crimea.

Fig. 2 in Four newly recorded species of planktonic cyanobacteria (Oscillatoriales, Cyanobacteria) in Korea

Fig. 2. Microscopic photographs of Planktothricoides raciborskii FBCC-A1472. (A, B) Arrangement of filament in the colony, (C, D) Sur- face of trichomes, (E-J) Apical cell of trichomes. Scale bars (A) 50 μm, (B) 20 μm, (C-J) 10 μm.

Fig. 3 in Four newly recorded species of planktonic cyanobacteria (Oscillatoriales, Cyanobacteria) in Korea

Fig. 3. Microscopic photographs of Planktothrix spiroides SJH-1. (A, B) Arrangement of filament in the colony, (C-J) Apical cell of trichomes. Scale bars (A, B) 20 μm, (C-J) 10 μm.

Fig. 1 in Four newly recorded species of planktonic cyanobacteria (Oscillatoriales, Cyanobacteria) in Korea

Fig. 1. Microscopic photographs of Laspinema thermale FBCC-A1475. (A, B) Arrangement of filament in the colony, (C-H) Apical cell of trichomes, (E) Necridic cell. Scale bars (A, B) 20 μm, (C-H) 10 μm.

Fig. 5 in Four newly recorded species of planktonic cyanobacteria (Oscillatoriales, Cyanobacteria) in Korea

Fig. 5. Maximum-Likelihood (ML) phylogenetic tree based on 16S rRNA gene sequences of Laspinema thermale, Planktothricoides raciborskii, Planktothrix spiroides, Cephalothrix lacustris, and other cyanobacterial strains. A 16S rRNA gene sequences of Gloeobacter violaceus (Gloeobacteraceae), Pseudanabaena catenata (Pseudanabaenaceae) were included as the outgroups. The support values at the nodes are written as follows: ML/Bayesian. Support values are displayed at nodes for>50% ML bootstrap proportions and>0.5 Bayesian posterior probability. The branch lengths are proportional to the scale given. Bold represents data obtained in this study.

Fig. 4 in Four newly recorded species of planktonic cyanobacteria (Oscillatoriales, Cyanobacteria) in Korea

Fig. 4. Microscopic photographs of Cephalothrix lacustris FBCC-A1473. (A, B) Arrangement of filament in the colony, (C-H) Apical cell of trichomes, (C, D, H, I, L) Aerotopes, (F-H, J-L) Apical cell strongly capitate with calyptra, (K) Necridic cell. Scale bars (A) 50 μm, (B) 20 μm, (C-L) 10 μm.

opencc-by-4.0Dec 2019View details →

Fig. 3 in Occurrence of sea lice, Caligus undulatus Shen and Li, 1959 (Copepoda: Siphonostomatoida: Caligidae) in plankton samples collected from Korea

Fig. 3. Caligus undulatus, adult female from Gangjin Bay, Korea. A. genital complex and abodomen, ventral. B. leg 1. C. tip of second exopodal segment of leg 1. D. leg 2. E. leg 3. F. first exopodal segment of leg 3. G, H. leg 4. I. leg 5. Scale bars: A = 200 μm; B-E, G = 100 μm; F, H, I = 50 μm.

opencc-by-4.0Dec 2019View details →

Fig. 4 in Occurrence of sea lice, Caligus undulatus Shen and Li, 1959 (Copepoda: Siphonostomatoida: Caligidae) in plankton samples collected from Korea

Fig. 4. Caligus undulatus, adult male from Mokpo Harbour, Korea. A. habitus, dorsal. B. urosome, dorsal. C. antenna. D. postantennal process. E. maxillule. F. post oral pad. G. maxilliped. H. sternal furca. I. genital segment and legs 5 and 6, ventral. Scale bars: A = 400 μm; B, I = 200 μm; C-H = 100 μm.

opencc-by-4.0May 2018View details →

Calibration of test diameter and area as proxies for body size in the planktonic foraminifera Globoconella puncticulata

Here we provide an extensive image library of Globoconella puncticulata, with accompanying 2D and 3D coordinate data and morphometric measurements.  This data was generated using high-throughput imaging methods (AutoMorph) developed in P.M. Hull's lab at Yale University. This dataset accompanies the manuscript: Brombacher, J.A., Elder, L.E., Hull, P.M., Wilson, P.A. and Ezard, T.H.(In Press) Calibration of test diameter and area as proxies for body size in the planktonic foraminifera Globoconella puncticulata. Journal of Foraminiferal Research. The manuscript describes important details related to data collection and usage and should be consulted before using the data provided here.  Samples were obtained from three sites in the Atlantic Ocean: equatorial Ocean Drilling Program (ODP) Site 925, subtropical ODP Site 659, and mid-latitude Integrated Ocean Drilling Program (IODP) Site U1313. 1233 individual foraminifera of the species Globoconella puncticulata were picked from these samples to be imaged. Nine slides of microfossils were imaged at multiple focal heights (z-planes; 31.1um step distance) using a light microscope with an automated stage and processed with the image processing models of AutoMorph. AutoMorph software and tutorials can be accessed here: https://github.com/HullLab. For an example of a raw slide scan see: Hsiang, Allison Y., Nelson, Kaylea, Elder, Leanne E., Liu, Yusu, & Hull, Pincelli M. (2016). Slide scan example for Automorph. Zenodo. http://doi.org/10.5281/zenodo.167557. Slides were named with the IODP or ODP site number. Each slide was imaged with the foraminifera arranged in 2-3 orientations (i.e., umbilical, spiral, and/or edge). One of the nine slide was imaged with both light and computed tomography in order to compare the volumetric data obtained from the two approaches. This slide had 6 individual foraminifera. All individuals imaged with this combination of approaches have ‘CTscan’ included in the file name. This AutoMorph/CT scanned slide was imaged from three orientations (umbilical, spiral, and edge) and with two z-step distances (distance between imaged focal planes on the z-axis) of 11.2 um and 31.31 um. Images and morphometric data are provided in 9 datasets detailed below. Do note: our slide scanning technique often identifies background light scatter and/or other slide debris (glue, shell fragments, etc.) as ‘objects’, and these objects are numbered in sequence. We have excluded all non-foraminiferal objects from the datasets below, so the object numbers of the foraminifera will often be discontinuous (i.e.: 2,3,4,10,11,16). 1) 2d_coordinates.tar provides the 2D coordinates of each successfully extracted orientation from the 1233 individual Globoconella puncticulata (2811 total successfully extracted orientations) in a single csv (all2dcoordinates.csv). 2d_coordinates.tar also provides a csv for each slide scan at a particular orientation (26 slide scans:  4 samples imaged in 3 orientations, 4 samples imaged in 2 orientations, and 1 sample imaged from 3 orientations with two different 2 Z-step sizes per orientations (i.e., 6 scans for the one sample)). 2) 2dmorph_data_all.tar contains all Globoconella puncticulata with 2D measurements extracted by the AutoMorph routine run2morph (2811 total successfully extracted orientations), and a text file listing all objects with failed 2D extractions and non-forminiferal objects. 3) 2d_outline_check.tar provides an overlay of the extracted 2D outline on the Globoconella puncticulata EDF for quality control purposes for all extracted Globoconella puncticulata (2811 total successfully extracted orientations). 5) 3d_obj_files.tar provides directories for each slide scan with the 3D mesh coordinates as obj files for each extracted Globoconella puncticulata (2270 total successfully extracted orientations). Note: more 3D extractions failed than 2D extractions, accounting for the difference in the number of 2D extractions (2811) and 3D extractions (2270). 6) 3d_pdfs.tar provides directories of each slide scan with the 3D pdfs of each Globoconella puncticulata extracted (2270 total successfully extracted orientations) for quality control purposes. 3D pdfs, meshes and shape measurements were generated by the AutoMorph module run3dmorph. Note that only some pdf viewers are able to display 3d pdfs properly.  4) 3dmorph_data.tar contains a csv file for each slide scan with the 3d measurements generated for each Globoconella puncticulata by the AutoMorph module run3dmorph (2270 total successfully extracted objects in 26 directories representing each slide scan at a particular orientation). 7) object_ edf_images.tar contains the extended depth of focus (EDF)images in 26-directories for each slide scan at a particular orientation. The EDFs are 2D image composites created from the z-stacked photographic images by the AutoMorph focus module. Together, the 26-directories contain 2811 total images representing the successfully extracted 2D orientations. 8) sampleID.csv is a csv of all sample information. This includes the Slide name for the physical slide each sample is on, the Object number on that slide scan for each foraminifera used in the study, and the Ocean Drilling Program information for each object. Ocean Drilling Program details consist of the Leg: the Leg number for the drilling cruise, Site: the Ocean Drilling Program collection site number, the Hole:  the drilling hole ID, the Core: the Core number from that drilling site, the core Type: the type of drilling equipment used (H for all these samples which is an advanced hydraulic piston core), the Section: the section number on the core, and the Top and Bottom: the sample top and bottom interval in cm from the top of the section.  9) slide_images_boxed.tar contains one image for each slide view at a particular orientation 26 slide scans:  4 samples imaged in 3 orientations, 4 samples imaged in 2 orientations, and 1 sample imaged from 3 orientations with two different 2 Z-step sizes per orientations (i.e., 6 scans for the one sample). A red box delineates each object extracted using the AutoMorph segment module. Slides are named according to their ocean drilling sample identification (see dataset #10). 10) z-stacks.tar.gz contains the original z-stack images of each Globoconella puncticulata (2811 total representing the successfully extracted 2D orientations) in 26 directories representing each slide scan at a particular orientation).

opencc-by-4.0Mar 2019View details →

Micro-CT scans, whole-test meshes, and internal chamber segments of planktonic foraminifera for three-dimensional analysis of inter- and intra-specific variation in ontogenetic growth trajectories

Here, we release tomographic reconstructions of 42 planktonic foraminifera from plankton tows and sediment traps, along with meshes and shrinkwrap meshes the whole tests and internal meshes of segmented chambers. Shrinkwrap meshes are test meshes that have been modified to close all pores and apertures in the test. Additionally, we have provided sample metadata for each specimen and volumetric measurements for the tests and chambers. This dataset was used in a study of ontogenetic growth in planktonic foraminifera and its variation within and among species.  The CT-scans and reconstructions were obtained at Naturalis Biodiversity Center in Leiden, the Netherlands with a Zeiss Xradia 520 Versa micro-CT scanner. The meshes and segments were created at Yale University. <ol> <li>Sample_Metadata.csv: Spreadsheet containing information on the sampling localities and dates for all specimens.</li> <li>Scan_data.csv: Spreadsheet containing metadata for all micro-CT scans including current strength, pixel size, voltage, image height, image width, and the number of images taken.</li> <li>Whole_Test_Measurements.csv:  Spreadsheet containing measurements of linear dimensions (axis1, axis2, axis 3), total number of chambers, calcite test volume, calcite test surface area, shrinkwrap volumes, and and shrinkwrap surface areas for all specimens.</li> <li>Chamber_Measurements.csv: Spreadsheet containing measurements of individual internal chamber segments, including position from the final chamber (F-chamber), position from the first chamber (Chamber), volume, and surface area.</li> <li>CT_Scan_Stacks.zip: reconstructed micro-CT image stacks (.tif files) for each specimen.</li> <li>Meshes.zip: Meshes of the test calcite, the shrinkwrap, and the internal chamber segments for each specimen (.stl 3D mesh files). Regular test meshes are named with the format “SampleID.stl”, and shrinkwrap meshes are named “SampleID-WRAP.stl”. Chamber meshes are named “SampleID-CH#.stl” and “SampleID-CH#-Wrap.stl”. Chambers are numbered in relation to their position from the final chamber, with “CH1” being the final chamber and “CH2” being the penultimate chamber.</li> </ol> This data is described and analyzed in the manuscript “Three-Dimensional Analysis of Inter- and Intraspecific Variation in Ontogenetic Growth Trajectories of Planktonic Foraminifera” submitted to the journal Marine Micropaleontology.

Fig. 5 in Insights on Short-term Blooms of Planktonic Ciliates, Provided by an Easily Recognised Genus: Cyrtostrombidium

Fig. 5. Autocorrelation function of the weekly abundance of Cyrtostrombidium at site C. Horizontal dashed lines indicate ~95% CI for significance of each autocorrelation value. The first autocorrelation is 1 by definition; it is the correlation of a sample with itself. Correlation for lags (weeks) 2, 3, and 4 falls beyond the 95% CI, indicating a persistence of 3 weeks for a peak in abundance.

Fig. 1 in Insights on Short-term Blooms of Planktonic Ciliates, Provided by an Easily Recognised Genus: Cyrtostrombidium

Fig. 1. Chautengo lagoon, México, indicating the location of 10 sites (black circles) where 5 seasonal samplings took place and the one grid site (C) where geostatistical analysis was conducted and long-term data were collected. Spatial distribution of Cyrtostrombidium abundance (as cells ml–1) is presented as bar graphs at the 10 sites, over 5 months (October, January, March, May and August). For long-term data on site C, see Fig. 2.

Fig. 2 in Planktonic Ciliates of the Neva Estuary (Baltic Sea): Community Structure and Spatial Distribution

Fig. 2. Two groups of samples, distinguished by ordination (MDS) on the basis of similarity of the ciliate community structure (p <0.05). Upper and lower parts of the inner Neva Estuary (white and grey symbols) slightly differed by community structure (Global R = 0.163).

Fig. 1 in Planktonic Ciliates of the Neva Estuary (Baltic Sea): Community Structure and Spatial Distribution

Fig. 1. Scheme of the inner Neva Estuary and location of sampling stations; modified from Telesh et al. (2008). Broken line indicates the storm-surge barrier.

opencc-by-4.0Dec 2016View details →

Fig. 7 in Micropaleontological Study Of The Gura Beliei Red Marls Formation From The Pietroșița Area (Turonian - Maastrichtian). Part Iii Campanian-Maastrichtian Planktonic Foraminifera

Fig. 7: 1-6, 10-15, 22-27 Rugotruncana subpennyi (Gandolfi 1955), Maastrichtian, Țâța Valley, PietroȘița, LPB.IV.12446; 7-9 Rugoglobigerina rugosa (Plummer1926), Maastrichtian, Țâța Valley, PietroȘița, LPB.IV.12411; 16-18 Globotruncanella saratogensis (Applin, 1920), Maastrichtian, Țâța Valley, PietroȘița, LPB.IV.12441; 19-21, 24-29 Rugotruncana subglaessneri (Gandolfi 1955), Maastrichtian, Țâța Valley, PietroȘița, LPB.IV. 12421 (All specimens x 90).

opencc-by-4.0Dec 2016View details →

Fig. 14 in Micropaleontological Study Of The Gura Beliei Red Marls Formation From The Pietroșița Area (Turonian - Maastrichtian). Part Iii Campanian-Maastrichtian Planktonic Foraminifera

Fig. 14: 1-3 Globotruncanella sarmientoi (Gandolfi 1955), Maastrichtian, Țâța Valley, PietroȘița, LPB.IV.12448; 4-12 Archaeoglobigerina blowi (Pessagno 1967), Maastrichtian, Țâța Valley, PietroȘița, LPB.IV.12449; 13-15 Rugoglobigerina pustulata Brönnimann 1952, Maastrichtian, Țâța Valley, PietroȘița, LPB.IV.12415; 16-24 Rugoglobigerina ordinaria (Subbotina 1953), Maastrichtian, Țâța Valley, PietroȘița, LPB.IV.12446; 25-29 Rugoglobigrerina kelleri (Subbotina 1953 Maastrichtian, Țâța Valley, PietroȘița, LPB.IV.12451; 30-31 Rugoglobigerina rotundata Brönnimann 1952 Maastrichtian, Țâța Valley, PietroȘița, LPB.IV.12416 (All specimens x 90).