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157 results for “outline”
An annotated high-content fluorescence microscopy dataset with EGFP-Galectin-3-stained cells and manually labelled outlines
<p>Here we present a benchmarking dataset of fluorescence microscopy images with EGFP-Galectin-3-stained cells together with annotations of their outlines. Images were randomly selected from an RNA interference screen with a modified U2OS osteosarcoma cell line, acquired on a Thermo Fischer CX7 high-content imaging system at 20x magnification. </p> <p>The dataset contains 60 images showing over 2000 labelled nuclear objects in total, which is sufficiently large to train well-performing neural networks for instance or semantic segmentation. It is pre-split into training, development and test set, each in a zip file. The dataset should be referred to as Aitslab_bioimaging2.</p> <p>For most of the images, nuclear staining and annotations have been published previously in the dataset Aitslab_bioimaging1 (https://doi.org/10.5281/zenodo.6657260). The conversion script to produce the png images from the C01 images was published together with this dataset.</p>
Geospatial data for Luquillo Mountains, Puerto Rico: Mean annual precipitation, elevation, watershed outlines, and rain gage locations
The data archive is here: https://doi.org/10.5066/F74F1PM2 please use this DOI when citing this data set. These geospatial data sets were developed as part of a new analysis of all known current and historical rain gages in the Luquillo Mountains, Puerto Rico published in the journal article Murphy, S.F., Stallard, R.F., Scholl, M.A., Gonzalez, G., and Torres-Sanchez, A.J., 2017, Reassessing rainfall in the Luquillo Mountains, Puerto Rico: Local and global ecohydrological implications: PLOS One 12(7): e0180987, p. 1-26, https://doi.org/10.1371/journal.pone.0180987. That article provides a revised map of mean annual precipitation developed using elevation regression functions and residual interpolation, and that map is presented here in a raster file. Most previous forest- and watershed-wide estimates of precipitation (and evapotranspiration, as inferred by a water balance) have assumed that precipitation increases consistently with elevation in the Luquillo Mountains; therefore, precipitation in leeward Luquillo watersheds has been overestimated by up to 40%.Because the Luquillo Mountains often serve as a wet tropical archetype in global assessments of basic ecohydrological processes, these revised estimates are relevant to regional and global assessments of runoff efficiency, hydrologic effects of reforestation, geomorphic processes, and climate change. \<para\> Support for this work was provided by grants BSR-8811902, DEB-9411973, DEB-9705814 , DEB-0080538, DEB-0218039 , DEB-0620910 , DEB-1239764, DEB-1546686, and DEB-1831952 from the National Science Foundation to the University of Puerto Rico as part of the Luquillo Long-Term Ecological Research Program. Additional support provided by the University of Puerto Rico and the International Institute of Tropical Forestry, USDA Forest Service.\</para\>
Coordinates tracing 2D outlines of beaks (birds and squid)
<p>Two-dimensional coordinates for lines traced onto images of beaks.</p> <ul> <li>This is a .zip archive xy coordinates (250 files, .txt); and a list of specimen names (1 file, .csv).</li> <li>All images traced in FIJI.</li> <li>For each specimen, there is a trace of the beak rostrum and a separate trace of the beak bite surface.</li> <li>Each trace file should be a list of xy coordinates that ends at the beak tip. This must be checked/verified/corrected for all files before running any analyses! I recommend visual inspection by plotting each beak dataset as a scatterplot in a color spectrum (rainbow, etc.).</li> <li>These were traced over pixel images, so each file has a different number of xy coordinates (depending on the pixel resolution/image size that was traced).</li> <li>All bird specimen images were downloaded from Phenome10k.org</li> <li>All cephalopod specimens were traced from images published in: <ul> <li>Xavier, J. C. & Cherel, Y. 2009 Cephalopod beak guide for the Southern Ocean. British Antarctic Survey.</li> </ul> </li> </ul>
Digital Elevation Models (DEMs) and lava outlines from the 2023 Litla-Hrútur eruption, Iceland, from Pléiades satellite stereoimages
<p><strong>Introduction:</strong></p><p>On the 10th of July 2023, at 16:40, an eruption started in the Reykjanes Peninsula, Iceland, next to the mountain "Litla-Hrútur". As part of the response, the CIEST2 french initiative was activated (Gouhier et al., 2022). Once activated, Pléiades stereoimages were tasked and scheduled for fast delivery within the area of Interest. On the 20th of August 2023 an additional stereopair of images from Pléiades was acquired and processed after the eruption had stopped.</p><p>Once acquired and delivered, the Pléiades images were processed following the methods described in the section below. This repository contains the near-real time results of DEMs, difference maps compared to a pre-eruption DEM, and lava outlines digitized from the difference map and the orthoimage.</p><p> </p><p><strong>Methods</strong>:</p><p>The Pléiades stereoimages were processed using the Ames StereoPipeline (ASP, Shean et al., 2016, see ASP branch in repository), yielding a DEM in 2x2m GSD and an orthoimage in 0.5x0.5m GSD. The processing was done using as only input the stereoimages and their orientation information, as Rational Polynomial Coefficients (RPCs). The <i>parallel_stereo </i>routine performs all the steps needed in the correlation of the stereoimages, yielding a pointcloud which is then interpolated using the routine <i>point2dem</i>. Besides default parameters, the <i>parallel_stereo</i> parameters used for creation of the DEMs were the standard parameters, plus the following ones: </p><p><i>--stereo-algorithm asp_mgm --corr-tile-size 300 --corr-timeout 900 --cost-mode 3 --subpixel-mode 9 --corr-kernel 7 7 --subpixel-kernel 15 15</i></p><p>Once the DEM was created, DEM co-registration was applying in order to align and minimize positional biases between the pre-eruption DEM and the Pléiades DEMs. We followed the co-registration method of Nuth & Kääb (2011), implemented by David Shean's co-registration routines (<a href="https://github.com/dshean/demcoreg">https://github.com/dshean/demcoreg</a>, Shean et al., 2016). The co-registration involved a horizontal and vertical shift of the Pléiades DEMs, as well as a planar tilt correction. The horizontal offset obtained from the DEM co-registration was also applied to the Pléiades orthoimages.</p><p>The pre-eruption DEM used for this study is a survey done on the 27th of September 2022, data collected Birgir Óskarsson and Robert A. Askew (Icelandic Institute of Natural History) and processed by Sydney R. Gunnarsson and Joaquín M.C. Belart (National Land Survey of Iceland). Metadata of this dataset is available here: https://gatt.lmi.is/geonetwork/srv/eng/catalog.search#/metadata/c59da6cf-18ee-44af-a085-afbad0de029a</p><p>Lava outlines were manually digitized from the co-registered Pléiades orthoimages, The lava outlines are available as GeoPackages in the "GPKG" branch of the repository.</p><p>At the moment, the results from Pléiades are used by the Institute of Earth Sciences of the Univesity of Iceland (Jarðvisindustofnun Háskoli Íslands) to estimate lava volumes and effusion rate, following the methods described in Pedersen et al. (2022). Please contact the authors if these data are intended to be used for a similar purpose, in order to avoid conflict of interests or duplicate work. We encourage collaboration and data sharing for the purpose of the monitoring of the eruption and for research applications.</p><p><strong>Data naming convention:</strong></p><p>faf_YYYYMMDD_hhmmss_hhmmss_*align.tif: DEM obtained from the processing, co-registered to the reference pre-eruption DEM.</p><p>faf_YYYYMMDD_hhmmss_hhmmss_*align_diff.tif: Difference of elevation between the Pléiades DEM and the pre-eruption DEM.</p><p>faf_YYYYMMDD_hhmm.gpkg: Polygon containing the lava outlines, extracted from the Pléiades orthoimage and the map of elevation difference.</p><p>0_faf_YYYYMMDD_hhmmss_hhmmss_*fig.png: A figure showing the latest map of elevation difference, overlaid with a hillshade of the latest Pléiades DEM and the latest lava outlines, result of the processing of the Pléiades stereoimages. The figure was created using the tool imviewer.py from the GitHub repository https://github.com/dshean/imview (Shean et al., 2016).</p><p><strong>Data Specifications:</strong></p><ul><li>Cartographic projection: ISN93 / Lambert 1993 (EPSG:3057, <a href="http://https:/epsg.io/3057">https://epsg.io/3057</a>)</li><li>Origin of Elevation: meters above GRS80 ellipsoid (WGS84)</li><li>Raster data format: GeoTIFF</li><li>Raster compression system: LZW</li><li>Vector data format: GeoPackage (<a href="https://www.geopackage.org/">https://www.geopackage.org/</a>)</li><li>Pléiades dataset includes only DEMs because the Pléiades ortho imagery is for licensed use only. Please contact the authors for further information on this.</li></ul><p><strong>Acknowledgements</strong>: </p><p>Pléiades images from July 2023 were provided under the CIEST² initiative (CIEST2 is part of ForM@Ter (<a href="https://en.poleterresolide.fr/">https://en.poleterresolide.fr/</a>). Pléiades images from August 2023 were provided under the CEOS Volcano Supersite (https://ceos.org/ourwork/workinggroups/disasters/gsnl/). Image Pléiades©CNES2023, distribution AIRBUS DS.</p><p><strong>Dataset Attribution</strong>:</p><p>This dataset is licensed under a <a href="https://creativecommons.org/licenses/by-nc/4.0/">Creative Commons CC BY-NC 4.0 International License</a> (Attribution-NonCommercial).</p><p><strong>Citation:</strong></p><p>Please cite this repository as described below:</p><p>Joaquin M.C. Belart, Virginie Pinel, Hannah. I. Reynolds, Etienne Berthier, & Sydney R. Gunnarson. (2023). Digital Elevation Models (DEMs) and lava outlines from the 2023 Litla-Hrútur eruption, Iceland, from Pléiades satellite stereoimages (1) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.10133203</p>
Morpho-sedimentary outlines displayed in Figures 1, S1, and S6-S15 of the article "Source-to-sink aeolian fluxes from arid landscape dynamics in the Lut Desert"
<p>Morpho-sedimentary outlines of the aeolian landforms in the Lut Desert.</p>
An annotated high-content fluorescence microscopy dataset with Hoechst 33342-stained nuclei and manually labelled outlines
<p>Here we present a benchmarking dataset of fluorescence microscopy images with Hoechst 33342-stained nuclei together with annotations of nuclei, nuclear fragments and micronuclei. Images were randomly selected from an RNA interference screen with a modified U2OS osteosarcoma cell line, acquired on a Thermo Fischer CX7 high-content imaging system at 20x magnification. Labelling was performed by a single annotator and reviewed by a biomedical expert.</p> <p>The dataset contains 50 images showing over 2000 labelled nuclear objects in total, which is sufficiently large to train well-performing neural networks for instance or semantic segmentation. It is pre-split into training, development and test set, each in a zip file. The dataset should be referred to as Aitslab_bioimaging1. A brief article describing the dataset is also available (Arvidsson M, Kazemi Rashed S, Aits S. <a href="https://doi.org/10.1016/j.dib.2022.108769">10.1016/j.dib.2022.108769</a> )</p> <p><strong>Dataset description:</strong></p> <p>Fluorescence microscopy images: original .C01 files and files converted to 8-bit .png format (Grayscale)</p> <p>Annotations: 24-bit .png format (RGB)</p> <p>Script used to convert C01 to png images: C01_to_png.py file with python code and readme.md file with instructions to run it</p>
Proglacial Lake Outlines for Kebnekaise (Sweden) from Rapid Eye Imagery
<p>Proglacial lake outlines from the Kebnekaise area (Sweden) that have been manually delineated from Rapid Eye imagery. See Dye et al. (2022) for further details.</p>
Digital Elevation Models, orthoimages and lava outlines of the 2021 Fagradalsfjall eruption: Results from near real-time photogrammetric monitoring
<p>This repository contains the data behind the work described in Pedersen et al (in review), specifically the Digital Elevation Models (DEMs), orthoimages and lava outlines created as part of the near-real time monitoring of the Fagradalsfjall 2021 eruption (SW-Iceland).</p> <p>The processing of the data is explained in detail in the Supplement S2 of Pedersen et al (2022).</p> <p>The data derived from Pléiades surveys includes only the DEMs and the lava outlines. The Pléiades-based orthoimages are subject to license. Please contact the authors for further information about this.</p> <p><strong>Convention for file naming:</strong></p> <p>Data: DEM, Ortho, Outline</p> <p>YYYYMMDD_HHMM: Date of acquisition</p> <p>Platform used: Helicopter (HEL), Pléiades (PLE), Hasselblad A6D (A6D)</p> <p>Origin of elevations in DEMs: meters above ellipsoid (zmae)</p> <p>Ground Sampling Distance: 2x2m (DEM) and 30x30cm (Ortho)</p> <p>Cartographic projection: isn93 (see cartographic specifications for further details)</p> <p> </p> <p><strong>Cartographic specifications:</strong></p> <p>Cartographic projection: ISN93/Lambert 1993 (EPSG: 3057, https://epsg.io/3057)</p> <p>Horizontal and vertical reference frame: The surveys after 18 April 2021 are in ISN2016/ISH2004, updated locally around the study area in April 2021 (after pre-eruptive deformations occurred). The rest of the surveys of late March and early April were created using several floating reference systems (see Supplement S3 for details), since no ground surveys were available during the first weeks of the data collection. The surveys of 23 March 2021, 31 March 2021 were re-procesed in Gouhier et al., 2022, using the survey done on 18 May 2021 as reference.</p> <p>Origin of elevations: Ellipsoid WGS84</p> <p>Raster data format: GeoTIFF</p> <p>Raster compression system: ZSTD (http://facebook.github.io/zstd/)</p> <p>Vector data format: GeoPackage (https://www.geopackage.org/)</p>
FS_TD_Outline Data
<p>This dataset contains outline data related to the Total Difference method developed by Cox et al. (2009), collected for the associated grant project listed below. The associated ReadME file describes the samples and data collection procedures for the attached dataset.</p>
FS_Orientation_Outline_Data
<p>The following dataset contains the resulting normalized coefficients of Elliptical Fourier Analyses on frontal sinus outline data related to varying cranial orientation, associated with the grant listed below. The associated ReadMe file describes the samples and data collection procedures for the archived dataset. </p>
Figure 2 in Parallel evolution in molar outline of murine rodents: the case of the extinct Malpaisomys insularis (Eastern Canary Islands)
Figure 2. Schematic representation of the modern and fossil murine rodents compared to Malpaisomys. Top, molecular phylogeny after Chevret (1994) and Chevret et al. (2001). A calibration of the time of divergence between taxa is given by reference to the divergence of the Rattus rattus lineage, estimated as having occurred 12 Mya (Chevret et al., 2001). The grey box includes the arvicanthine rodents, characterized by a herbivorous diet. Bottom, fossil lineages with investigated localities. Thick grey lines indicate taxa with stephanodont characteristics, thick black lines, complete stephanodonty. Crosses indicate extinct taxa.
Data set of dorsal halfed shield outlines of specimens of Meiura, from the publication "Morphological diversity in true and false crabs reveals a common middle ground – the megalopa phase"
<p>Data set, containing all reconstructed shield shapes, all from representatives of Meiura, included in the analysis of the manuscript "Morphological diversity in true and false crabs reveals a common middle ground – the megalopa phase". The data sheet, detailing data origin can be found in the supplementarty material of the publication.</p>
Shapefiles with the outline of maximum water spread resulting from the catastrophic release of the Kakhovka Reservoir after the destruction of the Kakhovka Hydroelectric Power Plant by Russian occupying forces
<p>The map is based on remote sensing data from Sentinel-2A (Processing Level L2A), dated June 8, June 13, and June 18, 2023, and Landsat-9 (Collection 2 Level-1), dated June 9, 2023. </p> <p>The following Sentinel-2 remote sensing data granules were used:<br>S2A_MSIL2A_20230608T084601_N0509_R107_T36TUS_20230608T132103.SAFE S2A_MSIL2A_20230608T084601_N0509_R107_T36TVS_20230608T132103.SAFE<br>S2A_MSIL2A_20230608T084601_N0509_R107_T36TWS_20230608T132103.SAFE<br>S2A_MSIL2A_20230608T084601_N0509_R107_T36TVT_20230608T132103.SAFE<br>S2B_MSIL2A_20230613T084609_N0509_R107_T36TUS_20230613T102806.SAFE<br>S2B_MSIL2A_20230613T084609_N0509_R107_T36TVS_20230613T102806.SAFE<br>S2B_MSIL2A_20230613T084609_N0509_R107_T36TWS_20230613T102806.SAFE<br>S2A_MSIL2A_20230618T084601_N0509_R107_T36TUS_20230618T151602.SAFE<br>S2A_MSIL2A_20230618T084601_N0509_R107_T36TVS_20230618T151602.SAFE<br>S2A_MSIL2A_20230618T084601_N0509_R107_T36TWS_20230618T151602.SAFE</p> <p>The following remote sensing data scenes from Landsat-9 were used:<br>LC09_L1TP_179028_20230609_20230610_02_T1<br>LC09_L1TP_179027_20230609_20230610_02_T1</p> <p>The contour of the maximum water spread was constructed using a method of manual visual interpretation of remote sensing data, relying on knowledge of the local terrain. We consciously chose not to use automated methods with water indices such as the Normalized Difference Water Index (NDWI) or the Modified Normalized Difference Water Index (MNDWI), as these do not effectively distinguish water surfaces in areas covered with forest or dense reed thickets. Similarly, we did not use the SRTM digital elevation model due to significant artifacts in the study area, where the model shows the height of the forest canopy instead of the ground surface in forested areas.</p> <p>For visual interpretation of Sentinel-2A remote sensing data, we used combinations of spectral bands NIR-Red-Green (8-4-3) and SWIR2-NIR-Green (12-8-3). For the visual interpretation of Landsat-9 remote sensing data, we used combinations of bands SWIR1-NIR-Red (6-5-4) and NIR-Red-Green (5-4-3). To better align the resolution of Sentinel-2A remote sensing data (10 m/pixel) with that of Landsat-9 (30 m/pixel), the latter's data was enhanced using the panchromatic channel (Band 8) through IHS-based pansharpening to 15 m/pixel. The pansharpening was performed using a custom bash script, utilizing command-line tools and utilities such as ImageMagick (<a href="https://imagemagick.org" rel="nofollow">https://imagemagick.org</a>), listgeo, and geotifcp (<a href="https://github.com/OSGeo/libgeotiff">https://github.com/OSGeo/libgeotiff</a>). To expedite the pansharpening process, both Landsat scenes were cropped to the study region and merged by bands using the gdal_translate and gdal_merge.py utilities from the GDAL library (<a href="https://gdal.org/" rel="nofollow">https://gdal.org/</a>). For convenience, the Sentinel-2A data tiles T36TUS, T36TVS, and T36TWS were also cropped and merged by bands using custom scripts available at <a href="https://doi.org/10.5281/zenodo.13205058" rel="nofollow">https://doi.org/10.5281/zenodo.13205058</a>.</p> <p>During visual interpretation, the above-mentioned remote sensing data were compared with satellite images acquired before the destruction of the Kakhovka Hydroelectric Power Plant. In particular, Landsat-9 remote sensing data were compared with Landsat-8 data from June 1, 2023, and Sentinel-2A data were compared with Sentinel-2B data from June 3, 2023.</p> <p>Repository files:<br>floodMax_UTM36N.zip — contains the shapefile in UTM36N projection (EPSG:32636);<br>floodMax_WGS84.zip — contains the shapefile in geographic coordinates in WGS84 (EPSG:4326);<br>floodMax_WGS84.geojson.zip — contains a GeoJSON file in WGS84 coordinates (EPSG:4326).</p> <div> <h1>Web version of the map</h1> </div> <p>The web version of the maximum water spread map is available at:<br><a href="https://yumoskalenko.github.io/floodmap_Kakhovka2023/" rel="nofollow">https://yumoskalenko.github.io/floodmap_Kakhovka2023/</a></p> <p> </p> <p>Embed code for the map on a webpage:</p> <div> <pre><code><iframe style="border: 1px solid black" src="https://yumoskalenko.github.io/floodmap_Kakhovka2023/index.html" marginwidth="0" marginheight="0" scrolling="no" width="100%" height="360" frameborder="0"></iframe> </code></pre> <div> </div> </div> <p><em><strong>This scientific and technical product was created by the scientists of the Black Sea Biosphere Reserve of the National Academy of Sciences of Ukraine during the implementation of research on the topic "Monitoring the condition of natural complexes of the Black Sea Biosphere Reserve (‘Chronicle of Nature’)" (state registration number 0121U109174).</strong></em></p>
Simulated data for Correspondence on NanoVar's performance outlined by Jiang T. et al.
<p>Simulated data were generated as described by Jiang et al. 2021 with several modifications due to the encountering of errors. Please refer to https://github.com/cytham/nv_benchmark_jiang/blob/main/commands.md for the commands to replicate the analysis.</p>
Text-fig. 6. Scanning electron micrographs of seeds of ericalean affinity (a–d) and seeds of uncertain affinity (e–i) from Zliv-Řídká Blana locality. a: Protovisnea sp. 1, rounded seed with the narrow elongate seed cavity flanked by two bulging regions of larger cells, no. NM-F 3177; b: Protovisnea sp. 2, angular seed with the narrow elongate seed cavity flanked by two bulging regions of larger cells, no. NM-F 3179; c, d: Eurya crassitesta, one seed split into two parts, no. NM-F 3211, c – surface cells of the seed coat are palisade, d – cross-section of the seed; e: Nympheaceae sp. 1, seed, no. NM-F 3636; f: Nympheaceae sp. 2, seed, no. NM-F 4634; g: Klikovispermum sp.1, seeds with irregular outline and smooth outer surface, no. NM-F 3203; h: Klikovispermum malechii, seed with an orange-segment shape, no. NM-F 3299; i: Taxon 35, seed, no. NM-F 3236. in Plant Mesofossils From The Late Cretaceous Klikov Formation, The Czech Republic
Text-fig. 6. Scanning electron micrographs of seeds of ericalean affinity (a–d) and seeds of uncertain affinity (e–i) from Zliv-Řídká Blana locality. a: Protovisnea sp. 1, rounded seed with the narrow elongate seed cavity flanked by two bulging regions of larger cells, no. NM-F 3177; b: Protovisnea sp. 2, angular seed with the narrow elongate seed cavity flanked by two bulging regions of larger cells, no. NM-F 3179; c, d: Eurya crassitesta, one seed split into two parts, no. NM-F 3211, c – surface cells of the seed coat are palisade, d – cross-section of the seed; e: Nympheaceae sp. 1, seed, no. NM-F 3636; f: Nympheaceae sp. 2, seed, no. NM-F 4634; g: Klikovispermum sp.1, seeds with irregular outline and smooth outer surface, no. NM-F 3203; h: Klikovispermum malechii, seed with an orange-segment shape, no. NM-F 3299; i: Taxon 35, seed, no. NM-F 3236.
Text-fig. 4. Scanning electron micrographs (a, c, e–k) and X-ray microtomographic orthoslices (b, d) of capsular fruits compose of five carpels from Zliv-Řídká Blana locality. a–d: Taxon 4, a – fruit elliptical in shape, no. NM-F 3188, b – young fruit with reminisce of free styles at top and showing central placentation of seeds, no. NM-F 3188, c – pentacarpellate capsules in apical view, no. NM-F 3188, d – fruit with five locules, no. NM-F 3235; e, f: Taxon 6, e – elongated fruit in lateral view, the persistent perianth at the base of the fruit (arrowhead), no. NM-F 3194, f – fruit in apical view, no. NM-F 3194; g, h: Taxon 5, g – elongated fruit in lateral view, no. NM-F 3193, h – fruit showing remains of a persistent calyx in the basal part (arrowhead), no. NM-F 3193; i–k: Taxon 7, i – pentacarpellate capsules of broadly elliptical shape, no. NM-F 4091, j – fruit, apical view, no. NM-F 4091, k – fruit with five seeds (arrowheads) ellipsoidal or triangular in outline and with a thick seed coat, no. NM-F 4091. in Plant Mesofossils From The Late Cretaceous Klikov Formation, The Czech Republic
Text-fig. 4. Scanning electron micrographs (a, c, e–k) and X-ray microtomographic orthoslices (b, d) of capsular fruits compose of five carpels from Zliv-Řídká Blana locality. a–d: Taxon 4, a – fruit elliptical in shape, no. NM-F 3188, b – young fruit with reminisce of free styles at top and showing central placentation of seeds, no. NM-F 3188, c – pentacarpellate capsules in apical view, no. NM-F 3188, d – fruit with five locules, no. NM-F 3235; e, f: Taxon 6, e – elongated fruit in lateral view, the persistent perianth at the base of the fruit (arrowhead), no. NM-F 3194, f – fruit in apical view, no. NM-F 3194; g, h: Taxon 5, g – elongated fruit in lateral view, no. NM-F 3193, h – fruit showing remains of a persistent calyx in the basal part (arrowhead), no. NM-F 3193; i–k: Taxon 7, i – pentacarpellate capsules of broadly elliptical shape, no. NM-F 4091, j – fruit, apical view, no. NM-F 4091, k – fruit with five seeds (arrowheads) ellipsoidal or triangular in outline and with a thick seed coat, no. NM-F 4091.
Text-fig. 7. Hamamelidoxylon crystalliferum sp. nov., UF 279-34464. a: Diffuse porous wood with exclusively solitary vessels, tending to be angular in outline, TS. b: Growth ring boundary, marked by radially narrowed fibers, latewood vessels narrower than earlywood vessels of the next ring, fibers thick-walled, no axial parenchyma visible, TS. c: Scalariform intervessel pits in narrow vessel (left), fibers with distinctly bordered pits, TLS. d: Scalariform perforation plate, tyloses (T) formation from marginal ray cell, TLS. e: Scalariform perforation plates with fewer than 15 bars (PP), RLS. f: Vessel-ray parenchyma pits with in A Diverse Assemblage Of Late Eocene Woods From Oregon, Western Usa
Text-fig. 7. Hamamelidoxylon crystalliferum sp. nov., UF 279-34464. a: Diffuse porous wood with exclusively solitary vessels, tending to be angular in outline, TS. b: Growth ring boundary, marked by radially narrowed fibers, latewood vessels narrower than earlywood vessels of the next ring, fibers thick-walled, no axial parenchyma visible, TS. c: Scalariform intervessel pits in narrow vessel (left), fibers with distinctly bordered pits, TLS. d: Scalariform perforation plate, tyloses (T) formation from marginal ray cell, TLS. e: Scalariform perforation plates with fewer than 15 bars (PP), RLS. f: Vessel-ray parenchyma pits with
Text-fig. 1. Pistacia terrazasae sp. nov., a: UF 279-85025; b–i: UF 279-24545. a: Ring-porous wood with widely spaced solitary earlywood vessels; latewood vessels in radial multiples of 4 or more and in clusters, TS. b: Growth ring boundary, fiber walls thin to thick, TS. c: Simple perforation plates, alternate intervessel pits, helical thickenings in vessels, TLS. d: Multiseriate rays to 4-seriate, tyloses in vessels, helical thickenings throughout body of vessel element, and alternate intervessel pitting, TLS. e: Vessel-ray parenchyma pitting with reduced borders, oval in outline, RLS. f: Marginal row of upright cells, one inflated and crystalliferous, procumbent body cells, RLS. g: Multiseriate rays mostly 3-seriate, occasionally 4-seriate, uniseriate rays usually <10 cells tall, TLS. h: Ray with enlarged crystalliferous marginal cell, to left of C, TLS. i: Ray with canal, TLS. Scale bars: 200 µm in a, g; 100 µm in b, d, h; 50 µm in c, i; 20 µm in e, f. in A Diverse Assemblage Of Late Eocene Woods From Oregon, Western Usa
Text-fig. 1. Pistacia terrazasae sp. nov., a: UF 279-85025; b–i: UF 279-24545. a: Ring-porous wood with widely spaced solitary earlywood vessels; latewood vessels in radial multiples of 4 or more and in clusters, TS. b: Growth ring boundary, fiber walls thin to thick, TS. c: Simple perforation plates, alternate intervessel pits, helical thickenings in vessels, TLS. d: Multiseriate rays to 4-seriate, tyloses in vessels, helical thickenings throughout body of vessel element, and alternate intervessel pitting, TLS. e: Vessel-ray parenchyma pitting with reduced borders, oval in outline, RLS. f: Marginal row of upright cells, one inflated and crystalliferous, procumbent body cells, RLS. g: Multiseriate rays mostly 3-seriate, occasionally 4-seriate, uniseriate rays usually <10 cells tall, TLS. h: Ray with enlarged crystalliferous marginal cell, to left of C, TLS. i: Ray with canal, TLS. Scale bars: 200 µm in a, g; 100 µm in b, d, h; 50 µm in c, i; 20 µm in e, f.
Text-fig. 4. Fagus dodgei sp. nov., a, b, d–h: UF 279-34468; c: UF 279-30165. a: Wood diffuse-porous to semi-ring-porous with distinct latewood zone with narrower vessels; vessels solitary and in short multiples; diffuse, diffuse-in-aggregates axial parenchyma visible in latewood, TS. b: Growth ring boundary, TS. c: Opposite intervessel pitting, TLS. d: Scalariform perforation plate with fewer than 10 bars, RLS. e: Simple perforation plates (PP), RLS. f: Vessel-ray parenchyma pitting with reduced borders and frequently oval in outline, RLS. g: Rays 1–4(–5)-seriate with variable numbers of marginal rows, TLS. h: Rays of two distinct sizes, widest rays>10-seriate, TLS. Scale bars: 200 µm in a, h; 100 µm in b, e, g; 50 µm in d, f. in A Diverse Assemblage Of Late Eocene Woods From Oregon, Western Usa
Text-fig. 4. Fagus dodgei sp. nov., a, b, d–h: UF 279-34468; c: UF 279-30165. a: Wood diffuse-porous to semi-ring-porous with distinct latewood zone with narrower vessels; vessels solitary and in short multiples; diffuse, diffuse-in-aggregates axial parenchyma visible in latewood, TS. b: Growth ring boundary, TS. c: Opposite intervessel pitting, TLS. d: Scalariform perforation plate with fewer than 10 bars, RLS. e: Simple perforation plates (PP), RLS. f: Vessel-ray parenchyma pitting with reduced borders and frequently oval in outline, RLS. g: Rays 1–4(–5)-seriate with variable numbers of marginal rows, TLS. h: Rays of two distinct sizes, widest rays>10-seriate, TLS. Scale bars: 200 µm in a, h; 100 µm in b, e, g; 50 µm in d, f.
Text-fig. 2. Celtis popsii sp. nov., UF 279-34460. a: Growth ring with earlywood of multiple rows of vessels solitary and in radial multiples; latewood vessels in wavy tangential bands, TS. b: Growth ring boundary, latewood vessels in multiples with axial parenchyma confluent, TS. c: Simple perforation plates, alternate intervessel pits, polygonal in outline, TLS. d: Vessel-ray parenchyma pits to right of VRP, oval in outline, with slightly reduced borders, RLS. e: Rays tending to two sizes, some multiseriate rays with distinct sheath cells, multiseriate rays usually with 1 marginal row of square to upright cells, occasionally with 4 or more; uniseriate rays less than 10 cells high, TLS. f: Detail of multiseriate ray with distinct sheath cells, vessel element end walls, TLS. Scale bars: 200 µm in a, e; 100 µm in b; 50 µm in c, f; 20 µm in d. in A Diverse Assemblage Of Late Eocene Woods From Oregon, Western Usa
Text-fig. 2. Celtis popsii sp. nov., UF 279-34460. a: Growth ring with earlywood of multiple rows of vessels solitary and in radial multiples; latewood vessels in wavy tangential bands, TS. b: Growth ring boundary, latewood vessels in multiples with axial parenchyma confluent, TS. c: Simple perforation plates, alternate intervessel pits, polygonal in outline, TLS. d: Vessel-ray parenchyma pits to right of VRP, oval in outline, with slightly reduced borders, RLS. e: Rays tending to two sizes, some multiseriate rays with distinct sheath cells, multiseriate rays usually with 1 marginal row of square to upright cells, occasionally with 4 or more; uniseriate rays less than 10 cells high, TLS. f: Detail of multiseriate ray with distinct sheath cells, vessel element end walls, TLS. Scale bars: 200 µm in a, e; 100 µm in b; 50 µm in c, f; 20 µm in d.
ScienceDex guides
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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.