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Transfer learning for galaxy feature detection: Finding Giant Star-forming Clumps in low redshift galaxies using Faster R-CNN
<p>This repository contains the data released in the paper 'Transfer learning for galaxy feature detection: Finding Giant Star-forming Clumps in low redshift galaxies using Faster R-CNN' <em>(DOI: <a href="https://doi.org/10.1093/rasti/rzae013">10.1093/rasti/rzae013</a>).</em></p> <p>We release a detailed catalogue of Giant Star-forming Clumps (GSFCs), detected for the full set of Galaxy Zoo: Clump Scout galaxies observed by SDSS using the Faster R-CNN architecture with the Zoobot classification-CNN as a feature extraction backbone.</p> <p>The final models and code are made publicly available via Github: <a href="https://github.com/ou-astrophysics/Faster-R-CNN-for-Galaxy-Zoo-Clump-Scout">https://github.com/ou-astrophysics/Faster-R-CNN-for-Galaxy-Zoo-Clump-Scout</a>.</p> <p>We will release updates if needed via Zenodo versioning. We recommend using the latest version of this repository. You can check the version you are currently viewing on the right-hand sidebar.</p> <p>Please cite the paper (DOI: <a href="https://doi.org/10.1093/rasti/rzae013">10.1093/rasti/rzae013</a>) when using the data in this repository.</p> <p>The csv-file <em>FRCNN_Zoobot_SDSS_GZCS_detections.csv</em> has the following columns. Alternatively, the file <em>FRCNN_Zoobot_SDSS_GZCS_detections.gzip</em> contains the same data but stored as a parquet-file.</p> <table> <tbody><tr> <th>Column name</th> <th>Description</th> </tr> </tbody><tbody> <tr> <td>specobjid</td> <td>SDSS spec object ID</td> </tr> <tr> <td>dr7objid</td> <td>SDSS DR7 object ID</td> </tr> <tr> <td>clump_id</td> <td>Clump index</td> </tr> <tr> <td>clump_label_id</td> <td>Clump label ID (1 or 2)</td> </tr> <tr> <td>clump_label_name</td> <td>Clump label name</td> </tr> <tr> <td>clump_score</td> <td>Detection score for the clump</td> </tr> <tr> <td>clump_centre_ra</td> <td>Clump centroid RA in degrees</td> </tr> <tr> <td>clump_centre_dec</td> <td>Clump centroid dec in degrees</td> </tr> <tr> <td>clump_flux_u</td> <td>Clump u-band flux in Jy</td> </tr> <tr> <td>clump_flux_g</td> <td>Clump g-band flux in Jy</td> </tr> <tr> <td>clump_flux_r</td> <td>Clump r-band flux in Jy</td> </tr> <tr> <td>clump_flux_i</td> <td>Clump i-band flux in Jy</td> </tr> <tr> <td>clump_flux_z</td> <td>Clump z-band flux in Jy</td> </tr> <tr> <td>clump_flux_err_u</td> <td>Clump u-band flux error in Jy</td> </tr> <tr> <td>clump_flux_err_g</td> <td>Clump g-band flux error in Jy</td> </tr> <tr> <td>clump_flux_err_r</td> <td>Clump r-band flux error in Jy</td> </tr> <tr> <td>clump_flux_err_i</td> <td>Clump i-band flux error in Jy</td> </tr> <tr> <td>clump_flux_err_z</td> <td>Clump z-band flux error in Jy</td> </tr> <tr> <td>clump_mag_u</td> <td>Clump u-band magnitude (AB-mag)</td> </tr> <tr> <td>clump_mag_g</td> <td>Clump g-band magnitude (AB-mag)</td> </tr> <tr> <td>clump_mag_r</td> <td>Clump r-band magnitude (AB-mag)</td> </tr> <tr> <td>clump_mag_i</td> <td>Clump i-band magnitude (AB-mag)</td> </tr> <tr> <td>clump_mag_z</td> <td>Clump z-band magnitude (AB-mag)</td> </tr> <tr> <td>clump_ext_mag_u</td> <td>Clump u-band extinction (E(B-V), AB-mag)</td> </tr> <tr> <td>clump_ext_mag_g</td> <td>Clump g-band extinction (E(B-V), AB-mag)</td> </tr> <tr> <td>clump_ext_mag_r</td> <td>Clump r-band extinction (E(B-V), AB-mag)</td> </tr> <tr> <td>clump_ext_mag_i</td> <td>Clump i-band extinction (E(B-V), AB-mag)</td> </tr> <tr> <td>clump_ext_mag_z</td> <td>Clump z-band extinction (E(B-V), AB-mag)</td> </tr> <tr> <td>clump_mag_corr_u</td> <td>Clump corrected u-band magnitude (AB-mag)</td> </tr> <tr> <td>clump_mag_corr_g</td> <td>Clump corrected g-band magnitude (AB-mag)</td> </tr> <tr> <td>clump_mag_corr_r</td> <td>Clump corrected r-band magnitude (AB-mag)</td> </tr> <tr> <td>clump_mag_corr_i</td> <td>Clump corrected i-band magnitude (AB-mag)</td> </tr> <tr> <td>clump_mag_corr_z</td> <td>Clump corrected z-band magnitude (AB-mag)</td> </tr> <tr> <td>clump_mag_corr_u_g</td> <td>Clump colour (u-g)</td> </tr> <tr> <td>clump_mag_corr_g_r</td> <td>Clump colour (g-r)</td> </tr> <tr> <td>clump_mag_corr_r_i</td> <td>Clump colour (r-i)</td> </tr> <tr> <td>clump_mag_corr_i_z</td> <td>Clump colour (i-z)</td> </tr> <tr> <td>clump_flux_ratio</td> <td>Est. clump/galaxy near-UV flux ratio (u-band)</td> </tr> <tr> <td>is_clump_3pct</td> <td>Flag (True/False) if clump/galaxy flux ratio is >3%</td> </tr> <tr> <td>is_clump_8pct</td> <td>Flag (True/False) if clump/galaxy flux ratio is >8%</td> </tr> <tr> <td>galaxy_ra</td> <td>Host galaxy RA in degrees</td> </tr> <tr> <td>galaxy_dec</td> <td>Host galaxy dec in degrees</td> </tr> <tr> <td>galaxy_z</td> <td>Host galaxy redshift</td> </tr> <tr> <td>galaxy_mag_u</td> <td>Host galaxy u-band magnitude (AB-mag)</td> </tr> <tr> <td>galaxy_mag_g</td> <td>Host galaxy g-band magnitude (AB-mag)</td> </tr> <tr> <td>galaxy_mag_r</td> <td>Host galaxy r-band magnitude (AB-mag)</td> </tr> <tr> <td>galaxy_mag_i</td> <td>Host galaxy i-band magnitude (AB-mag)</td> </tr> <tr> <td>galaxy_mag_z</td> <td>Host galaxy z-band magnitude (AB-mag)</td> </tr> <tr> <td>galaxy_mag_err_u</td> <td>Host galaxy u-band magnitude error (AB-mag)</td> </tr> <tr> <td>galaxy_mag_err_g</td> <td>Host galaxy g-band magnitude error (AB-mag)</td> </tr> <tr> <td>galaxy_mag_err_r</td> <td>Host galaxy r-band magnitude error (AB-mag)</td> </tr> <tr> <td>galaxy_mag_err_i</td> <td>Host galaxy i-band magnitude error (AB-mag)</td> </tr> <tr> <td>galaxy_mag_err_z</td> <td>Host galaxy z-band magnitude error (AB-mag)</td> </tr> <tr> <td>galaxy_flux_u</td> <td>Host galaxy u-band flux in Jy</td> </tr> <tr> <td>galaxy_flux_g</td> <td>Host galaxy g-band flux in Jy</td> </tr> <tr> <td>galaxy_flux_r</td> <td>Host galaxy r-band flux in Jy</td> </tr> <tr> <td>galaxy_flux_i</td> <td>Host galaxy i-band flux in Jy</td> </tr> <tr> <td>galaxy_flux_z</td> <td>Host galaxy z-band flux in Jy</td> </tr> <tr> <td>galaxy_expAB_r</td> <td>Host galaxy axis ratio from SDSS</td> </tr> <tr> <td>galaxy_expRad_r</td> <td>Host galaxy exponential fit scale radius from SDSS</td> </tr> <tr> <td>galaxy_lmass</td> <td>Host galaxy log mass in MSun</td> </tr> <tr> <td>galaxy_lssfr</td> <td>Host galaxy log specific SFR</td> </tr> <tr> <td>galaxy_mag_corr_u</td> <td>Host galaxy corrected u-band magnitude (AB-mag)</td> </tr> <tr> <td>galaxy_mag_corr_g</td> <td>Host galaxy corrected g-band magnitude (AB-mag)</td> </tr> <tr> <td>galaxy_mag_corr_r</td> <td>Host galaxy corrected r-band magnitude (AB-mag)</td> </tr> <tr> <td>galaxy_mag_corr_i</td> <td>Host galaxy corrected i-band magnitude (AB-mag)</td> </tr> <tr> <td>galaxy_mag_corr_z</td> <td>Host galaxy corrected z-band magnitude (AB-mag)</td> </tr> </tbody> </table> <p> </p>
Clumped Isotope Data from Gar Scale Bioapatite Samples and Lab Standards
<p>We measured the clumped isotope, Δ<sub>47</sub>, composition of the carbonate in the bioapatite of modern gar scales from 19 specimens collected from eight locations in North America, with mean water temperatures ranging from 11.3 to 27.0 °C. Samples were reacted at 90 °C and standards were reacted at both 25 °C and 90 °C. Samples and standards were run on a MAT 253 dual-inlet gas-source isotope ratio mass spectrometer (Thermo Scientific, USA) housed at the Yale University Analytical and Stable Isotope Center. Raw data was processed using the most up-to-date methods (Petersen et al., 2019). Our sample reproducibility was 0.021‰ (1 SD). Our standards included cylinder CO<sub>2 </sub>(Airgas, USA), CO<sub>2</sub> equilibrated with water at 25 °C and 50 °C, Carrara marble, and the ETH carbonate anchors. Δ<sub>47</sub> data is presented as ‰, InterCarb-Carbon Dioxide Equilibrium Scale (I-CDES) 90 °C for samples and standards reacted at 90 °C and I-CDES 25 °C for standards reacted at 25 °C.</p> <p> </p> <p>We use modern climate data from Daymet V4 (Thornton et al., 2022). We convert variable water temperatures into an effective temperature <em>T</em><sub>e</sub>, which accounts for the influence of temperature on growth rate. <em>T</em><sub>e</sub> for our gar samples ranges from 13.8 to 27.1 °C. We used this dataset to create a new calibration relating temperature to the Δ<sub>47</sub> in gar scale bioapatite. The resulting calibration curve is: Δ<sub>47</sub> = (0.1206 ± 0.0171) x 10<sup>6</sup>/<em>T</em><sub>e</sub><sup>2</sup> – (0.7429 ± 0.0587) (1 SE), with <em>R</em><sup>2</sup> = 0.75.</p>
Atmospheric clumped O2 isotope composition simulation data and analysis scripts from EMAC/aMC models
<p>This publication contains source code, data and analysis scripts/results of the simulations presented in the following manuscript:</p> <blockquote> <p>Laskar, A.H., G.A. Adnew, S.S. Gromov, R. Peethambaran, B. Steil, J. Lelieveld, T. Blunier and T. Röckmann (2022). "Large variations in atmospheric oxidants and temperature during the Holocene" (in review)</p> </blockquote> <p> </p> <p><strong>EMAC simulations analysis</strong></p> <p>The analysis contains integrals of species burdens and other atmospheric physicochemical parameters obtained with the clumped isotopes of oxygen (CIO)-enabled ECHAM/MESSy Atmospheric Chemistry model (EMAC, see <a href="https://www.messy-interface.org">MESSy consortium website</a> for more information) model in various climate states. Simulations were performed in 2021–2022 at the <a href="https://www.dkrz.de">German Climate Computing Centre</a> (DKRZ) with the support of the <a href="https://www.palmod.de">PalMod project</a>.</p> <p>Analysis data is stored in human/machine-readable file <code>D36-EMAC-analysis.dat</code>, please refer to its header for variables description, etc.</p> <p>Additional (to those presented in the manuscript) analysis plots from EMAC data analysis are available in <code>D36-EMAC-analysis.vsz</code> (see the hardcopy in <code>D36-EMAC-analysis.pdf</code>) prepared using the <a href="https://veusz.github.io">Veusz</a> software.</p> <p> </p> <p><strong>2BM/MC (two-box Monte-Carlo) model code, simulation data and analysis</strong></p> <p>2BM/MC code/simulation setup is implemented within the advanced Monte-Carlo framework (aMC) and is available in the <a href="https://gitlab.com/sergey.gromov/amc/-/tree/vpCIO">respective repository</a>. A copy of the source code used to perform simulations is provided here (see <code>aMC-vpCIO.tar.gz</code> archive).</p> <p>2BM/MC output is stored in the <a href="https://www.unidata.ucar.edu/software/netcdf/">netCDF format</a> (ver. 4) and can be read in by any compatible software. The output contains probe statistics (reference <em>probed</em> distributions of the variables) in <code>vpCIO-probe_stat-*.nc</code> and resulting statistics (distributions <em>matching</em> given criteria, i.e. changes to the Δ36 signature vs. PD conditions) in <code>vpCIO-delta-*.nc</code> files, respectively.</p> <p>We use <a href="https://ferret.pmel.noaa.gov">NOAA Ferret</a> software to derive additional statistics of the third parameter (viz. average STE (<em>S</em>) changes) over the obtained 2D frequency histograms of other parameters (viz. changes to equilibration rate (<em>Req)</em> and temperature (<em>Teq</em>)). The scripts exemplifying this calculation are presented in <code>D36-vpCIO-analysis__proc*</code> files, which output results/overview plots in <code>vpCIO-delta-*__proc.nc</code> and <code>vpCIO-delta-*.gif</code> files.</p> <p>The analysis of the 2BM/MC simulation is available in <code>D36-vpCIO-analysis.vsz</code> script (see the hardcopy in <code>D36-vpCIO-analysis.pdf</code>) prepared using the <a href="https://veusz.github.io">Veusz</a> software. Note that some plots require the abovementioned third-parameter statistics as input.</p> <p><strong>Performing simulations with 2BM/MC</strong></p> <p>In order to perform simulations (e.g. with altered parameters), please follow the <a href="https://gitlab.com/sergey.gromov/amc/-/tree/vpCIO#integrating-your-code-building-executing">respective guide</a> for and build the <code>aMC-vpCIO</code> model. A typical sequence of shell commands to build and run 2BM/MC (which is referred to as <code>vpCIO</code> generic model within the <code>aMC</code>) is:</p> <pre><code># clone the distribution and check-out `vpCIO` branch or particular commit referenced in the repository history [user@pc]/~> git clone https://gitlab.com/sergey.gromov/amc.git [user@pc]/~> cd amc [user@pc]/~/amc> git checkout vpCIO # or unpack the source code available in this publication: [user@pc]/~> tar -xvf `aMC-vpCIO.tar.gz` [user@pc]/~> cd amc # build the aMC/vpCIO model executable # (note that you need at least a GCC or Intel compiler suite and respective netCDF v.4 library Fortran interface available in your environment): [user@pc]/~/amc> make vpCIO # adjust model setup (see the `vpCIO/amc.nml` namelist) ... # perform simulation [user@pc]/~/amc> cd vpCIO [user@pc]/~/amc/vpCIO> ./xamc # calculate additional statistics/produce overview with NOAA Ferret: [user@pc]/~/amc/vpCIO> ferret -gif -script D36-vpCIO-analysis__proc.jnl MH [user@pc]/~/amc/vpCIO> ./D36-vpCIO-analysis__proc</code></pre> <p>Note that output files contain the build timestamp and repository commit hash for the code used in the simulation, e.g.:</p> <pre><code>[user@pc]/~/amc/vpCIO> ncdump -h ./vpCIO-delta-dMH.nc | grep 'build' :build = "vpCIO@https://gitlab.com/sergey.gromov/amc__aMC_v1.9-110-g2566229@2022-12-09T16:43:12+01:00__built@2022-12-09T16:48:03+01:00__<user>@<email.com>" ;</code></pre> <p> </p> <p>Please contact Sergey Gromov ( sergey.gromov (at) mpic.de ) for additional information and access to the original experiment data.</p> <p> </p>
Simulation data and software scripts used in calculus of ∆36 signature from EMAC clumped O2 isotope-inclusive model
<p>This publication contains simulation data and software scripts for calculating quantities related to clumped oxygen isotope signature (∆<sub>36</sub>) derivation, as described in the "static" framework of Yeung‍ et‍ al. (2016), hereinafter "Y16") and subsequently used in Yeung‍ et‍ al.‍ (2019) analysis. We provide the output of the 1950–2011 transient simulation with EMAC model with explicit "dynamic" simulation of ∆<sub>36</sub> (i.e. <sup>18</sup>O<sup>18</sup>O isotopologues undergoing transport, mixing and O(<sup>3</sup>P)-mediated isotope equilibration) to demonstrate the importance of several assumptions/simplifications involved in the static calculus.</p> <p> </p> <p>Please refer to .README.pdf for details.</p>
Data and Code for "Metal-enriched, sub-kiloparsec gas clumps in the circumgalactic medium of a faint z = 2.5 galaxy"
<p>This repository has code and data used in the paper "Metal-enriched, sub-kiloparsec gas clumps in the circumgalactic medium of a faint z = 2.5 galaxy" (http://arxiv.org/abs/1406.4239). If you find any of the data or code useful for a publication, please consider citing that paper.</p>
Clumped-isotope constraint on upper-tropospheric cooling during the Last Glacial Maximum
<p>Ice cores and other paleotemperature proxies, together with general circulation models, have provided information on past surface temperatures and the atmosphere's composition in different climates. Little is known, however, about past temperatures at high altitudes, which play a crucial role in Earth's radiative energy budget. Paleoclimate records at high-altitude sites are sparse, and the few that are available show poor agreement with climate model predictions. These disagreements could be due to insufficient spatial coverage, spatiotemporal biases, or model physics; new records that can mitigate or avoid these uncertainties are needed. Here, we constrain the change in upper-tropospheric temperature at the global scale during the Last Glacial Maximum (LGM) using the clumped-isotope composition of molecular oxygen trapped in polar ice cores. Aided by global three-dimensional chemical transport modeling, we exploit the intrinsic temperature sensitivity of the clumped-isotope composition of atmospheric oxygen to infer that the upper troposphere (effective mean altitude 10 – 11 km) was 6-9ºC cooler during the LGM than during the late preindustrial Holocene. A complementary energy balance approach supports a minor or negligible steepening of atmospheric lapse rates during the LGM, which is consistent with a range of climate model simulations. Proxy-model disagreements with other high-altitude records may stem from inaccuracies in regional hydroclimate simulation, possibly related to land-atmosphere feedbacks.</p>
Acid fractionation during carbonate digestion with phosphoric acid – Assessment of two different techniques applied for clumped and stable isotope analysis using a Tuneable Infrared Laser Differential Absorption Spectrometer (TILDAS) [dataset]
<p>Date files : </p> <table> <tbody> <tr> <td> <p>Data 1 (Relationship between Mixing ratio difference of sample and WRG and D638 value).xlsx;Data 2 (Role of bulk isotope composition (δ628 & δ636) on Δ638).xlsx;Data 3 (CDES scale conversion).xlsx;Data 4 (VPDB scale conversion for d628 and d636).xlsx;Data 5 (Reference material values).xlsx;Data 6 (Break seal method acid fractionation factor of calcite).xlsx;Data 7 (IAB method acid fractionation factor of calcite).xlsx</p> </td> </tr> </tbody> </table>
3D Parameter Maps of Red Clump Stars in the Milky Way -- Absolute Magnitudes and Intrinsic Colors
<p>Catalog, application and supplementary figures for the RC paper.</p> <p>1100mRC_WC2021new.fits.zip -- RC catalog</p> <p>Gaia photometric RC sample with 11 million RCs selected based on {\it Gaia}'s EDR3 parallax, our 3D parameter maps, and extinction--distance profile.</p> <p>ra, dec -- position; dm -- distance modulus; av -- V-band extinction</p> <p>dm1 -- corrected distance modulus; av1 -- corrected extinction. used for low-extinction RCs</p> <p>edm -- uncertainty of distance modulus; flag -- 1: high probability RCs, 0: low probability RCs.</p> <p> </p> <p>RC_calculator_linux.zip -- application RC2021 and installer for linux</p> <p>RC_calculator_mac.zip -- application RC2021 and installer for mac </p> <p>The application to estimate the absolute magnitudes and intrinsic colors for RCs with the APOGEE or LAMOST parameters</p> <p> </p> <p>eps -- the best applicable ranges for using application.</p> <p>pd_APOGEE.eps and pd_LAMOST.eps -- Probability densities of each parameter for absolute magnitude training set (orange) and the whole sample (blue). </p> <p>pd_APOGEE_color.eps and pd_LAMOST_color.eps -- Probability densities of each parameter for intrinsic color training set (orange) and the whole sample (blue). </p>
Text-fig. 41. Scanning electron microscope (SEM) images of monocolpate pollen of Piercipollis simplex gen. et sp. nov. from a pollen clump; Torres Vedras locality, Portugal. a) Holotype; pollen clump that yielded the pollen in this Text-figure; b–d) Pollen grains in distal (b), proximal (c) and lateral views (d) showing the very long colpus and the well-developed reticulum that is only loosely attached to the smooth surface of the foot layer; note the large angular lumina, smooth muri and short, sparsely scattered, columellae; note also that main body of pollen grains (foot layer) does not fill out the whole space of the reticulum; e) Reticulum showing the smooth muri loosely attached to the smooth surface of the foot layer by short, sparsely scattered, columellae. Specimen, TV44-S136755 (holotype). Scale bars 300 Μm (a), 6 Μm (b–d), 3 Μm (e). in The Early Cretaceous Mesofossil Flora Of Torres Vedras (Ne Of Forte Da Forca), Portugal: A Palaeofloristic Analysis Of An Early Angiosperm Community
Text-fig. 41. Scanning electron microscope (SEM) images of monocolpate pollen of Piercipollis simplex gen. et sp. nov. from a pollen clump; Torres Vedras locality, Portugal. a) Holotype; pollen clump that yielded the pollen in this Text-figure; b–d) Pollen grains in distal (b), proximal (c) and lateral views (d) showing the very long colpus and the well-developed reticulum that is only loosely attached to the smooth surface of the foot layer; note the large angular lumina, smooth muri and short, sparsely scattered, columellae; note also that main body of pollen grains (foot layer) does not fill out the whole space of the reticulum; e) Reticulum showing the smooth muri loosely attached to the smooth surface of the foot layer by short, sparsely scattered, columellae. Specimen, TV44-S136755 (holotype). Scale bars 300 Μm (a), 6 Μm (b–d), 3 Μm (e).
Text-fig. 35. Scanning electron microscope (SEM) images of a fruit of Pennicarpus sp. and monocolpate pollen of Pennipollis sp. from a pollen clump; Torres Vedras locality, Portugal. a) Fruit of Pennicarpus sp. showing the poorly preserved fruit wall enclosing a single seed; b) Pollen clump that yielded the pollen in this Text-figure (c, d); c, d) Pollen grains showing the loose reticulum bearing small spinules that are often in two rows; note the smooth surface of the foot layer, the absence of columellae, the continuous muri bordering the apertures and spiny orbicules (arrowheads). Specimens, TV38-S174609 (a), TV44-S148015 (b–d). Scale bars 300 Μm (a, b), 6 Μm (c, d). in The Early Cretaceous Mesofossil Flora Of Torres Vedras (Ne Of Forte Da Forca), Portugal: A Palaeofloristic Analysis Of An Early Angiosperm Community
Text-fig. 35. Scanning electron microscope (SEM) images of a fruit of Pennicarpus sp. and monocolpate pollen of Pennipollis sp. from a pollen clump; Torres Vedras locality, Portugal. a) Fruit of Pennicarpus sp. showing the poorly preserved fruit wall enclosing a single seed; b) Pollen clump that yielded the pollen in this Text-figure (c, d); c, d) Pollen grains showing the loose reticulum bearing small spinules that are often in two rows; note the smooth surface of the foot layer, the absence of columellae, the continuous muri bordering the apertures and spiny orbicules (arrowheads). Specimens, TV38-S174609 (a), TV44-S148015 (b–d). Scale bars 300 Μm (a, b), 6 Μm (c, d).
Text-fig. 39. Scanning electron microscope (SEM) images of monocolpate pollen of Eckhartia intermedia sp. nov. from a pollen clump, probably fragment of a stamen (a–e) and anthers and pollen of Eckhartia sp. (f–k); Torres Vedras locality, Portugal. a) Pollen clump that yielded the pollen in (b–e); b–d) Pollen grains viewed from distal (d) and proximal surfaces (b, c) showing the long colpus and well-developed reticulum with large and small luminae; e) Reticulum showing smooth muri supported by short columellae firmly attached to the smooth surface of the foot layer; note the occasional small luminae; f, g) Fragments of narrow elongate anthers with same kind of pollen as in (i); h) Inner surface of anther wall showing small spherical orbicules; in The Early Cretaceous Mesofossil Flora Of Torres Vedras (Ne Of Forte Da Forca), Portugal: A Palaeofloristic Analysis Of An Early Angiosperm Community
Text-fig. 39. Scanning electron microscope (SEM) images of monocolpate pollen of Eckhartia intermedia sp. nov. from a pollen clump, probably fragment of a stamen (a–e) and anthers and pollen of Eckhartia sp. (f–k); Torres Vedras locality, Portugal. a) Pollen clump that yielded the pollen in (b–e); b–d) Pollen grains viewed from distal (d) and proximal surfaces (b, c) showing the long colpus and well-developed reticulum with large and small luminae; e) Reticulum showing smooth muri supported by short columellae firmly attached to the smooth surface of the foot layer; note the occasional small luminae; f, g) Fragments of narrow elongate anthers with same kind of pollen as in (i); h) Inner surface of anther wall showing small spherical orbicules;
Text-fig. 55. Scanning electron microscope (SEM) images of stamen fragments and pollen of Ibrahimia verminculata (a–h) and unnamed pantoporate pollen from pollen clump (i); Torres Vedras locality, Portugal. a) Holotype; stamen fragment that yielded the pollen in (b–f); b–f) Pantoporate pollen grains with vermiculate tectum and regularly spaced microechinate and pores with verrucate aperture membranes; g) Stamen fragment that yielded the pollen in (h); h) Abraded pantoporate pollen with vermiculate tectum and regularly spaced microechinate; i) Pantoporate pollen from coprolite with microreticulate-foveolate tectum and verrucate aperture membranes. Specimens, TV44-S148019 (holotype; a–f), TV44- S136782 (g, h), TV142-S170216 (i). Scale bars 300 Μm (a, g), 15 Μm (b), 6 Μm (d, e, h, i), 1.5 Μm (c, f). in The Early Cretaceous Mesofossil Flora Of Torres Vedras (Ne Of Forte Da Forca), Portugal: A Palaeofloristic Analysis Of An Early Angiosperm Community
Text-fig. 55. Scanning electron microscope (SEM) images of stamen fragments and pollen of Ibrahimia verminculata (a–h) and unnamed pantoporate pollen from pollen clump (i); Torres Vedras locality, Portugal. a) Holotype; stamen fragment that yielded the pollen in (b–f); b–f) Pantoporate pollen grains with vermiculate tectum and regularly spaced microechinate and pores with verrucate aperture membranes; g) Stamen fragment that yielded the pollen in (h); h) Abraded pantoporate pollen with vermiculate tectum and regularly spaced microechinate; i) Pantoporate pollen from coprolite with microreticulate-foveolate tectum and verrucate aperture membranes. Specimens, TV44-S148019 (holotype; a–f), TV44- S136782 (g, h), TV142-S170216 (i). Scale bars 300 Μm (a, g), 15 Μm (b), 6 Μm (d, e, h, i), 1.5 Μm (c, f).
Text-fig. 52. Scanning electron microscope (SEM) images of tricolpate pollen of Samylinaea punctata gen. et sp. nov from a pollen clump; Torres Vedras locality, Portugal. a) Pollen clump (probable stamen fragment) that yielded the pollen in this Text-figure; b) Polar view of pollen grain showing two colpi, granular aperture membrane, and punctate tectum; c) Orbicule showing very finely granular surface; d) Pollen wall showing short columellae, well-developed punctate tectum and slightly thinner foot layer; e–h) Pollen grains showing punctate tectum and the folds associated with the irregular development of the colpi. Specimen, TV44-S174565 (holotype; a–h). Scale bars 300 Μm (a), 6 Μm (b, e–h), 3 Μm (c, d). in The Early Cretaceous Mesofossil Flora Of Torres Vedras (Ne Of Forte Da Forca), Portugal: A Palaeofloristic Analysis Of An Early Angiosperm Community
Text-fig. 52. Scanning electron microscope (SEM) images of tricolpate pollen of Samylinaea punctata gen. et sp. nov from a pollen clump; Torres Vedras locality, Portugal. a) Pollen clump (probable stamen fragment) that yielded the pollen in this Text-figure; b) Polar view of pollen grain showing two colpi, granular aperture membrane, and punctate tectum; c) Orbicule showing very finely granular surface; d) Pollen wall showing short columellae, well-developed punctate tectum and slightly thinner foot layer; e–h) Pollen grains showing punctate tectum and the folds associated with the irregular development of the colpi. Specimen, TV44-S174565 (holotype; a–h). Scale bars 300 Μm (a), 6 Μm (b, e–h), 3 Μm (c, d).
Text-fig. 31. Scanning electron microscope (SEM) images of monocolpate pollen of Burgeria striata gen. et sp. nov. from a pollen clump; Torres Vedras locality, Portugal. a) Holotype; pollen clump that yielded the pollen in this Text-figure; b) Pollen grains showing the distal colpus and the undulating tectum perforated by scattered punctae; c–e) Equatorial (c) and distal views (d, e) of pollen grains showing the long distal colpus with granular ornamentation and the undulating tectum perforated by scattered punctae; f) Detail of section through pollen wall showing thick tectum with fine striate ornamentation, perforated by punctae and supported by short stout columellae attached to the thin foot layer; g–h) Surface of tectum (g) and orbicule (h) showing fine striate ornamentation. Specimen, TV44-S149216 (holotype). Scale bars 300 Μm (a), 30 Μm (b), 6 Μm (c–e), 1.5 Μm (f–h). in The Early Cretaceous Mesofossil Flora Of Torres Vedras (Ne Of Forte Da Forca), Portugal: A Palaeofloristic Analysis Of An Early Angiosperm Community
Text-fig. 31. Scanning electron microscope (SEM) images of monocolpate pollen of Burgeria striata gen. et sp. nov. from a pollen clump; Torres Vedras locality, Portugal. a) Holotype; pollen clump that yielded the pollen in this Text-figure; b) Pollen grains showing the distal colpus and the undulating tectum perforated by scattered punctae; c–e) Equatorial (c) and distal views (d, e) of pollen grains showing the long distal colpus with granular ornamentation and the undulating tectum perforated by scattered punctae; f) Detail of section through pollen wall showing thick tectum with fine striate ornamentation, perforated by punctae and supported by short stout columellae attached to the thin foot layer; g–h) Surface of tectum (g) and orbicule (h) showing fine striate ornamentation. Specimen, TV44-S149216 (holotype). Scale bars 300 Μm (a), 30 Μm (b), 6 Μm (c–e), 1.5 Μm (f–h).
Text-fig. 32. Scanning electron microscope (SEM) images of monocolpate pollen of Burgeria striata gen. et sp. nov. from a pollen clump; Torres Vedras locality, Portugal. a) Pollen clump that yielded the pollen in this Text-figure; b) Pollen surface showing fine striate ornamentation; c–e) Pollen grains showing broad distal colpus with distinct granular ornamentation and the undulating tectum perforated by scattered punctae; note the very different sizes of pollen grains in the same pollen clump. Specimen, TV44-S174620. Scale bars 300 Μm (a), 6 Μm (c–e), 1.5 Μm (b). in The Early Cretaceous Mesofossil Flora Of Torres Vedras (Ne Of Forte Da Forca), Portugal: A Palaeofloristic Analysis Of An Early Angiosperm Community
Text-fig. 32. Scanning electron microscope (SEM) images of monocolpate pollen of Burgeria striata gen. et sp. nov. from a pollen clump; Torres Vedras locality, Portugal. a) Pollen clump that yielded the pollen in this Text-figure; b) Pollen surface showing fine striate ornamentation; c–e) Pollen grains showing broad distal colpus with distinct granular ornamentation and the undulating tectum perforated by scattered punctae; note the very different sizes of pollen grains in the same pollen clump. Specimen, TV44-S174620. Scale bars 300 Μm (a), 6 Μm (c–e), 1.5 Μm (b).
Text-fig. 30. Scanning electron microscope (SEM) images of monocolpate pollen of Dejaxia brevicolpites gen. et sp. nov. from a pollen clump; Torres Vedras locality, Portugal. a) Holotype; pollen clump (possible single pollen sac) that yielded the pollen in this Textfigure; b, c) Group of almost spherical pollen grains showing the irregularly undulating psilate tectum and abundant orbicules; d–g) Pollen grains showing the short colpi with a granular aperture membrane (d, f) and the irregularly undulating psilate tectum with scattered small perforations; note abundant orbicules (g); h) Pollen grain in proximal view showing the irregularly undulating psilate tectum resulting from the depressions around the perforations in the pollen wall. Specimen, TV44-S137909 (holotype). Scale bars 300 Μm (a), 30 Μm (b), 12 Μm (c), 6 Μm (d–h). in The Early Cretaceous Mesofossil Flora Of Torres Vedras (Ne Of Forte Da Forca), Portugal: A Palaeofloristic Analysis Of An Early Angiosperm Community
Text-fig. 30. Scanning electron microscope (SEM) images of monocolpate pollen of Dejaxia brevicolpites gen. et sp. nov. from a pollen clump; Torres Vedras locality, Portugal. a) Holotype; pollen clump (possible single pollen sac) that yielded the pollen in this Textfigure; b, c) Group of almost spherical pollen grains showing the irregularly undulating psilate tectum and abundant orbicules; d–g) Pollen grains showing the short colpi with a granular aperture membrane (d, f) and the irregularly undulating psilate tectum with scattered small perforations; note abundant orbicules (g); h) Pollen grain in proximal view showing the irregularly undulating psilate tectum resulting from the depressions around the perforations in the pollen wall. Specimen, TV44-S137909 (holotype). Scale bars 300 Μm (a), 30 Μm (b), 12 Μm (c), 6 Μm (d–h).
Text-fig. 8. Scanning electron microscope (SEM) images of spores from clumps of spores and sporangia with affinities to polypodiopsids (a–c) and of uncertain affinity (d–k); Torres Vedras locality, Portugal. a) Folded Cyathidites minor spores in proximal view showing trilete mark, from clump of spores; b) Cyathidites minor spores in proximal view showing trilete mark, from group of sporangia; c) Cyathidites australis spores in proximal view showing trilete mark, from group of sporangia; d–f) Linear group of spore masses (d; probable sporangial contents) composed of Taurocusporites segmentatus spores showing distal surface (e, middle) with concentric regions and proximal surface with segmented laesurae of elongated granules (e, right; f); in The Early Cretaceous Mesofossil Flora Of Torres Vedras (Ne Of Forte Da Forca), Portugal: A Palaeofloristic Analysis Of An Early Angiosperm Community
Text-fig. 8. Scanning electron microscope (SEM) images of spores from clumps of spores and sporangia with affinities to polypodiopsids (a–c) and of uncertain affinity (d–k); Torres Vedras locality, Portugal. a) Folded Cyathidites minor spores in proximal view showing trilete mark, from clump of spores; b) Cyathidites minor spores in proximal view showing trilete mark, from group of sporangia; c) Cyathidites australis spores in proximal view showing trilete mark, from group of sporangia; d–f) Linear group of spore masses (d; probable sporangial contents) composed of Taurocusporites segmentatus spores showing distal surface (e, middle) with concentric regions and proximal surface with segmented laesurae of elongated granules (e, right; f);
Text-fig. 7. Scanning electron microscope (SEM) images of spores with possible affinities to lycopodiopsids (a–c) and Schizaeaceae (d–g); Torres Vedras locality, Portugal. a) Densoisporites sp. from a clump of spores in proximal (left) and partial distal views (right) showing the narrow equatorial flange, long laesurae, and reticulum that is coarser on the distal surface than on the proximal surface; b, c) Unnamed microspores from clump of microspores in proximal (b) and distal (c) views showing finely reticulate surface; d, e) Cicatricosisporites ventusus fertile pinnules showing numerous attached sporangia (d) each with terminal annulus (arrowheads) and spores in situ (e); f) Cicatricosisporites sp. 1 spores from fertile pinnules bearing sporangia with a terminal in The Early Cretaceous Mesofossil Flora Of Torres Vedras (Ne Of Forte Da Forca), Portugal: A Palaeofloristic Analysis Of An Early Angiosperm Community
Text-fig. 7. Scanning electron microscope (SEM) images of spores with possible affinities to lycopodiopsids (a–c) and Schizaeaceae (d–g); Torres Vedras locality, Portugal. a) Densoisporites sp. from a clump of spores in proximal (left) and partial distal views (right) showing the narrow equatorial flange, long laesurae, and reticulum that is coarser on the distal surface than on the proximal surface; b, c) Unnamed microspores from clump of microspores in proximal (b) and distal (c) views showing finely reticulate surface; d, e) Cicatricosisporites ventusus fertile pinnules showing numerous attached sporangia (d) each with terminal annulus (arrowheads) and spores in situ (e); f) Cicatricosisporites sp. 1 spores from fertile pinnules bearing sporangia with a terminal
Text-fig. 13. Scanning electron microscope (SEM) images of pollen or spore clump with pollen grains or spores of unknown affinity that occur separately or adhering together in dyads, triads and tetrads; Torres Vedras locality, Portugal. a) Clump of pollen or spores that yielded the pollen or spores in this Text-figure; b–f) Grains adhering together in twos, threes or fours (b–e) or occurring singly and apparently with a proximal trilete mark (f); note that the adhering grains are connected by a smooth bandlike covering, perhaps remains of the microspore mother cell; note also abundant orbicules of various sizes among and over the grains. Specimen, TV44-S148149. Scale bars 300 Μm (a), 30 Μm (b–f). in The Early Cretaceous Mesofossil Flora Of Torres Vedras (Ne Of Forte Da Forca), Portugal: A Palaeofloristic Analysis Of An Early Angiosperm Community
Text-fig. 13. Scanning electron microscope (SEM) images of pollen or spore clump with pollen grains or spores of unknown affinity that occur separately or adhering together in dyads, triads and tetrads; Torres Vedras locality, Portugal. a) Clump of pollen or spores that yielded the pollen or spores in this Text-figure; b–f) Grains adhering together in twos, threes or fours (b–e) or occurring singly and apparently with a proximal trilete mark (f); note that the adhering grains are connected by a smooth bandlike covering, perhaps remains of the microspore mother cell; note also abundant orbicules of various sizes among and over the grains. Specimen, TV44-S148149. Scale bars 300 Μm (a), 30 Μm (b–f).
Text-fig. 10. Scanning electron microscope (SEM) images of conifer seeds (a, b) and pollen (c) and monoporate pollen of unknown affinity (d–j); Torres Vedras locality, Portugal. a, b) Unnamed conifer seeds (conifer seed sp. 1); c) Clump of bisaccate pollen grains; d) Fragment with microsporangia that yielded the pollen in (e–j); e, f, h) Monoporate pollen grains folded in various ways, exposing the tiny pore (e, h, arrowheads) or resembling a monocolpate grain (f); g) Detail of pollen grain showing pore (arrowhead) and finely rugulate exine surface that reflects the reticulate infratectal layer beneath the thin tectum; i) Detail of pore showing very slightly thickened margin; j) Spherical orbicules on the surface of two grains. Specimens, TV44-S174594 (a), TV44-S174595 (b), TV44-S174573 (c), TV44-S137904 (d–j). Scale bars 1 mm (a, b), 300 Μm (d), 100 Μm (c), 6 Μm (e, f, h), 3 Μm (g, j), 1.5 Μm (i). in The Early Cretaceous Mesofossil Flora Of Torres Vedras (Ne Of Forte Da Forca), Portugal: A Palaeofloristic Analysis Of An Early Angiosperm Community
Text-fig. 10. Scanning electron microscope (SEM) images of conifer seeds (a, b) and pollen (c) and monoporate pollen of unknown affinity (d–j); Torres Vedras locality, Portugal. a, b) Unnamed conifer seeds (conifer seed sp. 1); c) Clump of bisaccate pollen grains; d) Fragment with microsporangia that yielded the pollen in (e–j); e, f, h) Monoporate pollen grains folded in various ways, exposing the tiny pore (e, h, arrowheads) or resembling a monocolpate grain (f); g) Detail of pollen grain showing pore (arrowhead) and finely rugulate exine surface that reflects the reticulate infratectal layer beneath the thin tectum; i) Detail of pore showing very slightly thickened margin; j) Spherical orbicules on the surface of two grains. Specimens, TV44-S174594 (a), TV44-S174595 (b), TV44-S174573 (c), TV44-S137904 (d–j). Scale bars 1 mm (a, b), 300 Μm (d), 100 Μm (c), 6 Μm (e, f, h), 3 Μm (g, j), 1.5 Μm (i).
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.