Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
73
datasets available to search
ShareScore release 0.9.0
Dataset results
73 results for “localization microscopy”
In vivo rat brain for Ultrasound Localization Microscopy: raw and beamformed data.
<p><strong>Datasets provided for Open Platform for Ultrasound Localization Microscopy: Performance Assessment of Localization Algorithms.</strong></p> <p><strong>Abstract:</strong></p> <p>Ultrasound Localization Microscopy (<strong>ULM</strong>) is an ultrasound imaging technique that relies on the acoustic response of sub-wavelength ultrasound scatterers to map the microcirculation with an order of magnitude increase in resolution. Initially demonstrated <em>in vitro</em>, this technique has matured and sees implementation<em> in vivo</em> for vascular imaging of organs, and tumors in both animal models and humans. The performance of the localization algorithm greatly defines the quality of vascular mapping. We compiled and implemented a collection of ultrasound localization algorithms and devised three datasets<em> in silico</em> and<em> in vivo</em> to compare their performance through 18 metrics. We also present two novel algorithms designed to increase speed and performance. By openly providing a complete package to perform ULM with the algorithms, the datasets used, and the metrics, we aim to give researchers a tool to identify the optimal localization algorithm for their usage, benchmark their software and enhance the overall image quality in the field while uncovering its limits.</p> <p>This article provides all materials and post-processing scripts and functions.</p> <p><strong>Methods:</strong></p> <p>200.000 ultrasound images have been acquired <em>in vivo </em>on a rat brain with skull removal at 1000 Hz with a 15 MHz linear probe.</p> <p>This dataset contains raw radiofrequency data (<strong>RF</strong>) and beamformed images (<strong>IQ</strong>) of the brain vascularization with flowing microbubbles (ultrasound contrast agent).</p> <p><strong>Article to be cited:</strong> Heiles, Chavignon, Hingot, Lopez, Teston and Couture.<br> <a href="http://doi.org/10.1038/s41551-021-00824-8"><em>Performance benchmarking of microbubble-localization algorithms for ultrasound localization microscopy</em>, Nature Biomedical Engineering, 2022, (doi.org/10.1038/s41551-021-00824-8)</a>.</p> <p><strong>Related processing scripts and codes:</strong> <a href="https://github.com/AChavignon/PALA">github.com/AChavignon/PALA</a></p> <p><strong>Related datasets:</strong> <a href="https://doi.org/10.5281/zenodo.4343435">doi.org/10.5281/zenodo.4343435</a></p> <p><strong>Acknowledgments:</strong></p> <p>We thank Cyrille Orset (INSERM UMR-S U1237, Physiopathology and Imaging of Neurological Disorders, GIP Cyceron, BB@C, Caen, France) for animals’ preparation and perfusion of contrast agent and the biomedical imaging platform CYCERON (UMS 3408 Unicaen/CNRS, Caen, France).</p>
Super-Resolved FRET Imaging by Confocal Fluorescence-Lifetime Single-Molecule Localization Microscopy
<p>FRET-based methods are a special tool for detecting interactions between (bio)molecules and their immediate environment. The spatial distribution of molecular interactions and functional states can be seen using FLIM (Fluorescence Lifetime IMaging) and FRET imaging. The spatial information, accuracy, and dynamic range of the observed signals are, however, constrained by the fact that conventional FLIM and FRET imaging only provides average information over an ensemble of molecules within a diffraction-limited volume. On the other hand, conventional Single Molecule Localization Microscopy (SMLM) relies on highly sensitive multi-pixel detectors (e.g. sCMOS or EM-CCD) whose time resolution is not suitable for fluorescence lifetime measurements.</p> <p>Here, we demonstrate a method for obtaining super-resolved FRET imaging using confocal fluorescence-lifetime single-molecule localization microscopy. The proof of concept was carried out using a DNA origami sample for performing DNA-PAINT measurements in combination with fluorogenic probes for reducing background signal. With this method, We show that FRET events separated by sub-diffraction distances can be distinguished based on lifetime modifications.</p>
Deep and complex vascular anatomy in the rat brain described with Ultrasound Localization Microscopy in 3D
<p><strong>Abstract:</strong></p><p>Ultrasound Localization Microscopy (<strong>ULM</strong>) enables imaging microvessels in the brain with a resolution of a few tens of micrometers <i>in vivo</i>. The planar architecture of arterioles and venules was revealed with a 2D ultrasound scanner in the cortex of the rat brain. However, deeper in the brain, where the vascularization becomes tri-dimensional, 2D imaging remains limited by the elevation projection. In this study, volumetric ultrasound imaging was performed in the craniotomized rat brain to yield 3D ULM<i> in vivo</i> within 7.5 min of acquisition with a commercial system. For instance, it highlighted the thalamus or the circle of Willis with small vessels down to 21 µm. Microbubbles tracking also gave access to the 3D velocity vector of blood flow allowing to distinguish flow directions. Volumetric ULM resolved deep complex tri-dimensional vascular structures and was compared to 2D ULM. It is a safe, simple and repeatable system to image wide field of view in the brain.</p><p><strong>Data Description:</strong></p><p>Microbubbles have been detected, localized, and tracking with 3D ultrasound imaging <i>in vivo</i> in a rat brain with skull removal.</p><p>Individual microbubble trajectories are described in 4 columns vectores: <strong>[z, x, y, time]</strong> for each position of the path. Space positions are given in [mm], and times are given in [ms]. Trajectories data are stored in .mat files (<strong>tracks_0xx.mat </strong>and zipped inside <strong>tracks.zip</strong>) as cell arrays.</p><p>Tracks can be binned inside a volumetric grid with the sample code (<strong>ULM_rendering.m</strong>).</p><p><strong>Reference to be cited: </strong>Chavignon, Heiles, Hingot, Orset, Vivien and Couture.</p><p><i>Deep and complex vascular anatomy in the rat brain described with Ultrasound Localization Microscopy in 3D.</i><br> </p>
Raw data (RF) provided for : Sensing Ultrasound Localization Microscopy reveals glomeruli in rats and humans
<p><strong>Abstract :</strong> Estimation of glomerular function is a key element in the diagnosis of kidney disease. However, the study of glomeruli in the clinic remains indirect through urine and blood tests. Recent imaging technique called Ultrasound Localization Microscopy (ULM) originated from the ability to record continuous movements of individual microbubbles in the bloodstream. Although it improved the resolution of vascular imaging up to tenfold, the imaging of the smallest vessels had yet to be reported.</p> <p>We acquired ultrasound sequences from living humans and rats and then applied filtering dividing the data set into slow-moving and fast-moving microbubbles. We performed a double tracking to highlight and characterize this new population of microbubbles with singular behaviors: we called this technique “sensing ULM” (sULM). We used post-mortem micro-CT for side-by-side confirmation in rats.</p> <p>In this study, we report the observation of microbubbles flowing in capillaries bundles, i.e. the glomeruli, in the kidney in living humans and rats. We introduce a set of analysis tools dedicated to extracting quantitative information from individual microbubbles, like the remanence time or the normalized distance.</p> <p>As glomeruli play a key role in kidney function, their observation could yield a deeper understanding of kidney diseases and provide a diagnostic tool for patients. More generally, it will bring imaging capabilities closer to the functional units of organs, which is one of the keys to understanding most diseases, like cancers, diabetes, or kidney failures. </p> <p><strong>Academic reference to be cited : </strong>Denis, Bodard, Hingot, Chavignon, Battaglia, Renault, Lager, Aissani, Hélénon, Correas, and Couture. <em>Sensing Ultrasound Localization Microscopy reveals glomeruli in rats and humans,</em> eBioMedicine, 2023.</p> <p><strong>Article</strong> : <a href="https://www.thelancet.com/journals/ebiom/article/PIIS2352-3964(23)00143-3/fulltext">https://www.thelancet.com/journals/ebiom/article/PIIS2352-3964(23)00143-3/fulltext</a></p> <p><strong>Related scripts and software application</strong> : <a href="https://github.com/EngineerJB/akebia">https://github.com/EngineerJB/akebia</a></p> <p><strong>Beamformed dataset</strong> : <a href="../record/6811910#.ZA9dV3bMLid">https://zenodo.org/record/6811910#.ZA9dV3bMLid</a></p> <p><strong>Corresponding authors : </strong></p> <ul> <li>Article : Louise Denis, <a href="mailto:louise.denis@sorbonne-universite.fr">louise.denis@sorbonne-universite.fr</a>, Sylvain Bodard, <a href="mailto:sylvain.bodard@aphp.fr">sylvain.bodard@aphp.fr</a></li> <li>Scripts, and codes : Louise Denis, <a href="mailto:louise.denis@sorbonne-universite.fr">louise.denis@sorbonne-universite.fr</a>, Jacques Battaglia, <a href="mailto:jacques.battaglia@sorbonne-universite.fr">jacques.battaglia@sorbonne-universite.fr</a></li> <li>Materials, collaborations, rights and others: Olivier Couture, <a href="mailto:olivier.couture@sorbonne-universite.fr">olivier.couture@sorbonne-universite.fr</a></li> </ul>
Dataset provided for : Sensing Ultrasound Localization Microscopy reveals glomeruli in rats and humans
<p><strong>Abstract :</strong> Estimation of glomerular function is a key element in the diagnosis of kidney disease. However, the study of glomeruli in the clinic remains indirect through urine and blood tests. Recent imaging technique called Ultrasound Localization Microscopy (ULM) originated from the ability to record continuous movements of individual microbubbles in the bloodstream. Although it improved the resolution of vascular imaging up to tenfold, the imaging of the smallest vessels had yet to be reported.</p> <p>We acquired ultrasound sequences from living humans and rats and then applied filtering dividing the data set into slow-moving and fast-moving microbubbles. We performed a double tracking to highlight and characterize this new population of microbubbles with singular behaviors: we called this technique “sensing ULM” (sULM). We used post-mortem micro-CT for side-by-side confirmation in rats.</p> <p>In this study, we report the observation of microbubbles flowing in capillaries bundles, i.e. the glomeruli, in the kidney in living humans and rats. We introduce a set of analysis tools dedicated to extracting quantitative information from individual microbubbles, like the remanence time or the normalized distance.</p> <p>As glomeruli play a key role in kidney function, their observation could yield a deeper understanding of kidney diseases and provide a diagnostic tool for patients. More generally, it will bring imaging capabilities closer to the functional units of organs, which is one of the keys to understanding most diseases, like cancers, diabetes, or kidney failures. </p> <p><strong>Academic reference to be cited : </strong>Denis, Bodard, Hingot, Chavignon, Battaglia, Renault, Lager, Aissani, Hélénon, Correas, and Couture. <em>Sensing Ultrasound Localization Microscopy reveals glomeruli in rats and humans,</em> eBioMedicine, 2023.</p> <p><strong>Related scripts and software application</strong> : <a href="https://github.com/EngineerJB/akebia">https://github.com/EngineerJB/akebia</a></p> <p><strong>(New ! published in June 2024) Raw data :</strong> <a href="../records/11395562">https://zenodo.org/records/11395562</a></p> <p><strong>Corresponding authors : </strong></p> <ul> <li>Article : Louise Denis, <a href="mailto:louise.denis@sorbonne-universite.fr">louise.denis@sorbonne-universite.fr</a>, Sylvain Bodard, <a href="mailto:sylvain.bodard@aphp.fr">sylvain.bodard@aphp.fr</a></li> <li>Scripts, and codes : Louise Denis, <a href="mailto:louise.denis@sorbonne-universite.fr">louise.denis@sorbonne-universite.fr</a>, Jacques Battaglia, <a href="mailto:jacques.battaglia@sorbonne-universite.fr">jacques.battaglia@sorbonne-universite.fr</a></li> <li>Materials, collaborations, rights and others: Olivier Couture, <a href="mailto:olivier.couture@sorbonne-universite.fr">olivier.couture@sorbonne-universite.fr</a></li> </ul>
Enabling spectrally resolved single-molecule localization microscopy at high emitter densities: Dataset
<p>The data in this dataset accompanies the various figures present in the publication 'Enabling spectrally resolved single-molecule localization microscopy at high emitter densities'. Contained are tiff files used to create the figures 2-4 and Supplementary figures 1 and 2, as well as csvs after processed with the steps described in the paper (and contained in protocol text files).</p>
Text-fig. 7. Scanning electron micrographs (a, b, d, e, g–k), X-ray microtomographic orthoslices (c) and synchrotron radiation X-ray tomographic microscopy orthoslices (f) of fruits and endocarps of uncertain affinity from Zliv-Řídká Blana locality. a–c: Trebecenia sarcocalis, a – tricarpellate fruit, no. NM-F 3637, b – fruits supported by pentamerous and persistent calyx, no. NMF 3637, c – fruit almost circular in transverse section, no. NM-F 3637; d: Taxon 17, small fruit with slightly sunken stylar region, no. NM-F 3201; e: Taxon 19, spherical fruit, the fruit wall composed of large isodiametric, thick walled cells, no. NM-F 3181; f: Taxon 19, single-seeded fruit, no. NM-F 3621; g: Taxon 20, syncarpous, multicarpellate fruit of ten carpels, no. NM-F 3200; h: Taxon 22, syncarpous, multicarpellate fruit of seven carpels, no. NM-F 3159; i: cf. Sabia menispermoides, endocarp of drupaceous fruits, no. NM-F 4624; j: Taxon 25, endocarp triangular in cross-section, no. NM-F 3218; k: Taxon 24, endocarp spherical in cross-section with a distinctly ribbed and foveolate surface, no. NM-F 3217. in Plant Mesofossils From The Late Cretaceous Klikov Formation, The Czech Republic
Text-fig. 7. Scanning electron micrographs (a, b, d, e, g–k), X-ray microtomographic orthoslices (c) and synchrotron radiation X-ray tomographic microscopy orthoslices (f) of fruits and endocarps of uncertain affinity from Zliv-Řídká Blana locality. a–c: Trebecenia sarcocalis, a – tricarpellate fruit, no. NM-F 3637, b – fruits supported by pentamerous and persistent calyx, no. NMF 3637, c – fruit almost circular in transverse section, no. NM-F 3637; d: Taxon 17, small fruit with slightly sunken stylar region, no. NM-F 3201; e: Taxon 19, spherical fruit, the fruit wall composed of large isodiametric, thick walled cells, no. NM-F 3181; f: Taxon 19, single-seeded fruit, no. NM-F 3621; g: Taxon 20, syncarpous, multicarpellate fruit of ten carpels, no. NM-F 3200; h: Taxon 22, syncarpous, multicarpellate fruit of seven carpels, no. NM-F 3159; i: cf. Sabia menispermoides, endocarp of drupaceous fruits, no. NM-F 4624; j: Taxon 25, endocarp triangular in cross-section, no. NM-F 3218; k: Taxon 24, endocarp spherical in cross-section with a distinctly ribbed and foveolate surface, no. NM-F 3217.
Flat-Field Super-Resolution Localization Microscopy with a Low-Cost Refractive Beam-Shaping Element
<p>Raw data for the article "Flat-Field Super-Resolution Localization Microscopy with a Low-Cost Refractive Beam-Shaping Element". Each set of three files is a set of dSTORM images, taken using either top-hat illumination or a Gaussian illumination. For Sample 0, the top-hat illumination was performed first. For Sample 1, the Gaussian illumination was performed first.</p>
Autonomous Illumination Control for Localization Microscopy - Data
<p>Data and scripts associated with the manuscript entitled "Autonomous Illumination Control in Localization Microscopy."</p>
2D and 3D Segmentation of uncertain local collagen fiber orientations in SHG microscopy
<p><strong>General</strong></p> <p>This dataset consists out of multiple Second Harmonic Generation (SHG) microscopy scans of collagen fibers in mice bones. Some mices are diseased with osteogenesis imperfecta (brittle bone).</p> <p>We used this data to investigate the segmentation of uncertain local collagen fiber orientations. The corresponding paper "2D and 3D Segmentation of uncertain local collagen fiber orientations in SHG microscopy" is accepted at GCPR 2019.</p> <p><strong>Abstract</strong></p> <p>Collagen fiber orientations in bones, visible with Second Harmonic Generation (SHG) microscopy, represent the inner structure and its alteration due to influences like cancer. While analyses of these orientations are valuable for medical research, it is not feasible to analyze the needed large amounts of local orientations manually. Since we have uncertain borders for these local orientations only rough regions can be segmented instead of a pixel-wise segmentation. We analyze the effect of these uncertain borders on human performance by a user study. Furthermore, we compare a variety of 2D and 3D methods such as classical approaches like Fourier analysis with state-of-the-art deep neural networks for the classification of local fiber orientations. We present a general way to use pretrained 2D weights in 3D neural networks, such as Inception-ResNet-3D a 3D extension of Inception-ResNet-v2. In a 10 fold cross-validation our two stage segmentation based on Inception-ResNet-3D and transferred 2D ImageNet weights achieves a human comparable accuracy.</p> <p><strong>Links</strong></p> <p>A preprint of the paper is available at <a href="https://arxiv.org/abs/1907.12868">https://arxiv.org/abs/1907.12868</a>.</p> <p>The final publication is available at Springer via <a href="https://doi.org/10.1007/978-3-030-33676-9_26">https://doi.org/10.1007/978-3-030-33676-9_26</a></p> <p>The source code is available at <a href="https://github.com/Emprime/uncertain-fiber-segmentation">https://github.com/Emprime/uncertain-fiber-segmentation</a>.</p> <p><strong>Data description</strong></p> <p>Please read the accompanying paper for more information about the dataset. Please see the source code for more information about the usage of the data.</p> <ul> <li>shg-ce-de: contains the enhanced and denoised scans as image slices, the scans are sorted by mice (wt wildtyp, het ill mice), scan location and individual scan</li> <li>shg-masks: contains the ground truth masks for the three different classes (similar - Green, dissimilar - Red, not of interest - blue)</li> <li>shg-featues: contains the input and gt for the second stage of the proposed two stage segmentation</li> <li>shg-cross-splits: contains the 10 random splits for the 10 fold cross validation</li> <li>logs-prediction: contains the 10 tensorboard logs, weights and predictions for the 10 fold cross validations</li> </ul>
Text-fig. 3. Scanning electron micrographs (a, b) and synchrotron radiation X-ray tomographic microscopy orthoslices (c–e) of flower of Lambertiflora elegans gen. et sp. nov. from the Early Cretaceous Puddledock locality, Virginia, USA (holotype, PP53796, Puddledock sample 082). a) Flower in lateral view showing long pedicel and overlapping elongated tepals; b) Detail of flower showing overlapping elongated tepals; note the numerous holes indicating the position of probable secretory cells; c) Flower in longitudinal section showing overlapping elongated tepals, remains of probable poorly developed stamens or staminodes and probable poorly developed carpels on the central conical gynoecial region of the receptacle (cut between orthoslices xz0510 and 0570); d) Flower in longitudinal section (comparable to c) showing overlapping tepals, poorly developed stamens or staminodes, and probable poorly developed carpels on the central conical gynoecial region of the receptacle; note the prominent cavities from secretory cells scattered through the tissues (cut between orthoslice xz0560 and 0575); e) Flower in transverse section showing overlapping tepals, poorly developed stamens or staminodes, and remains of probable poorly developed carpels (cut between orthoslices xy1160 and 1180). Scale bars = 1 mm (a), 500 µm (b–e). in Multiparted, Apocarpous Flowers From The Early Cretaceous Of Eastern North America And Portugal
Text-fig. 3. Scanning electron micrographs (a, b) and synchrotron radiation X-ray tomographic microscopy orthoslices (c–e) of flower of Lambertiflora elegans gen. et sp. nov. from the Early Cretaceous Puddledock locality, Virginia, USA (holotype, PP53796, Puddledock sample 082). a) Flower in lateral view showing long pedicel and overlapping elongated tepals; b) Detail of flower showing overlapping elongated tepals; note the numerous holes indicating the position of probable secretory cells; c) Flower in longitudinal section showing overlapping elongated tepals, remains of probable poorly developed stamens or staminodes and probable poorly developed carpels on the central conical gynoecial region of the receptacle (cut between orthoslices xz0510 and 0570); d) Flower in longitudinal section (comparable to c) showing overlapping tepals, poorly developed stamens or staminodes, and probable poorly developed carpels on the central conical gynoecial region of the receptacle; note the prominent cavities from secretory cells scattered through the tissues (cut between orthoslice xz0560 and 0575); e) Flower in transverse section showing overlapping tepals, poorly developed stamens or staminodes, and remains of probable poorly developed carpels (cut between orthoslices xy1160 and 1180). Scale bars = 1 mm (a), 500 µm (b–e).
Text-fig. 2. Synchrotron radiation X-ray tomographic microscopy volume renderings (a, b) and orthoslices (c–e) of Mugideiriflora portugallica gen. et sp. nov. from the Early Cretaceous Catefica locality, Portugal (holotype, S174254, Catefica sample 150). Yellow dots – stamens, red dots – carpels. a) Flower in lateral view showing the broad bases of the laminar tepals; b) Flower in longitudinal section showing the flat to slightly concave floral receptacle with a central conical gynoecial region (cut between orthoslices yz0800 and 1220); c) Flower in transverse section showing the numerous laminar tepals in several series and the stamens cut in the region of the poorly differentiated anthers; note cellular differences between outer (op) and inner (in) perianth parts, as well as and transverse sections of anthers, apparently with laterally to slightly dorsally placed pollen sacs (arrow heads) (cut at orthoslice xy0770); d) Flower in transverse section showing the numerous laminar tepals in several series, flattened rhomboidal stamen bases in several series, and poorly differentiated carpels (cut at orthoslice xy0820); e) Flower in transverse section showing the numerous laminar tepals in several series, flattened rhomboidal stamen bases in several series, and poorly differentiated carpels (cut at orthoslice xy0920); f) Flower in longitudinal section showing the shallowly concave floral receptacle with laminar tepals, stamens, and a central conical gynoecial region bearing poorly differentiated carpels (cut at orthoslice yz0900); g) Flower in longitudinal section perpendicular to that in (f) showing stamens and poorly differentiated carpels (cut at orthoslice xz1630). Scale bars = 1 mm (a, b), 500 µm (c–g). in Multiparted, Apocarpous Flowers From The Early Cretaceous Of Eastern North America And Portugal
Text-fig. 2. Synchrotron radiation X-ray tomographic microscopy volume renderings (a, b) and orthoslices (c–e) of Mugideiriflora portugallica gen. et sp. nov. from the Early Cretaceous Catefica locality, Portugal (holotype, S174254, Catefica sample 150). Yellow dots – stamens, red dots – carpels. a) Flower in lateral view showing the broad bases of the laminar tepals; b) Flower in longitudinal section showing the flat to slightly concave floral receptacle with a central conical gynoecial region (cut between orthoslices yz0800 and 1220); c) Flower in transverse section showing the numerous laminar tepals in several series and the stamens cut in the region of the poorly differentiated anthers; note cellular differences between outer (op) and inner (in) perianth parts, as well as and transverse sections of anthers, apparently with laterally to slightly dorsally placed pollen sacs (arrow heads) (cut at orthoslice xy0770); d) Flower in transverse section showing the numerous laminar tepals in several series, flattened rhomboidal stamen bases in several series, and poorly differentiated carpels (cut at orthoslice xy0820); e) Flower in transverse section showing the numerous laminar tepals in several series, flattened rhomboidal stamen bases in several series, and poorly differentiated carpels (cut at orthoslice xy0920); f) Flower in longitudinal section showing the shallowly concave floral receptacle with laminar tepals, stamens, and a central conical gynoecial region bearing poorly differentiated carpels (cut at orthoslice yz0900); g) Flower in longitudinal section perpendicular to that in (f) showing stamens and poorly differentiated carpels (cut at orthoslice xz1630). Scale bars = 1 mm (a, b), 500 µm (c–g).
Text-fig. 5. Scanning electron micrographs (d–g) and synchrotron radiation X-ray tomographic microscopy orthoslices (a–c) of flowers of Atlantocarpus virginiensis gen. et sp. nov. (a–d: holotype, PP43780, Puddledock sample 156), Atlantocarpus sp. from the Early Cretaceous Buarcos locality (e, f: S105025, Buarcos sample 244) and receptacle of Atlantocarpus? from the Early Cretaceous Vale de Água locality (g: S101300, Vale de Água sample 141). a) Flower in lateral view showing scar from a single bract (br), attachment scars of tepals (t) and stamens (st) on the expanded basal portion of elongated receptacle and young carpels; b) Flower in lateral view showing expanded basal portion of the elongated receptacle and young carpels; c) Flower in longitudinal section showing expanded basal portion of the elongated receptacle and young carpels; note the irregular, possibly expanded stigmatic region (arrow heads), (orthoslice yz0340); d) Flower in lateral view showing attachment scars of tepals (t) and stamens (st) on the expanded basal portion of elongated receptacle and young carpels with possible grooved stigmatic regions (arrow heads); e) Flower in lateral view showing expanded basal portion of elongated receptacle and young carpels; f) Detail of flower in (e) showing in Multiparted, Apocarpous Flowers From The Early Cretaceous Of Eastern North America And Portugal
Text-fig. 5. Scanning electron micrographs (d–g) and synchrotron radiation X-ray tomographic microscopy orthoslices (a–c) of flowers of Atlantocarpus virginiensis gen. et sp. nov. (a–d: holotype, PP43780, Puddledock sample 156), Atlantocarpus sp. from the Early Cretaceous Buarcos locality (e, f: S105025, Buarcos sample 244) and receptacle of Atlantocarpus? from the Early Cretaceous Vale de Água locality (g: S101300, Vale de Água sample 141). a) Flower in lateral view showing scar from a single bract (br), attachment scars of tepals (t) and stamens (st) on the expanded basal portion of elongated receptacle and young carpels; b) Flower in lateral view showing expanded basal portion of the elongated receptacle and young carpels; c) Flower in longitudinal section showing expanded basal portion of the elongated receptacle and young carpels; note the irregular, possibly expanded stigmatic region (arrow heads), (orthoslice yz0340); d) Flower in lateral view showing attachment scars of tepals (t) and stamens (st) on the expanded basal portion of elongated receptacle and young carpels with possible grooved stigmatic regions (arrow heads); e) Flower in lateral view showing expanded basal portion of elongated receptacle and young carpels; f) Detail of flower in (e) showing
Text-fig. 4. Synchrotron radiation X-ray tomographic microscopy orthoslices of flowers of Lambertiflora virginiense gen. et sp. nov. from the Early Cretaceous Puddledock locality, Virginia, USA (holotype, PP53796, Puddledock sample 081). White dots – tepals, yellow dots – stamens or staminodes, red dot – central conical gynoecial region. a) Flower in longitudinal section showing elongated overlapping tepals, remains of probable poorly developed stamens or staminodes and probable poorly developed carpels on the central conical gynoecial region of the receptacle (orthoslice yz0454); b) Flower in transverse section showing rhomboidal bases of 30 tepals, nine poorly developed stamens or staminodes, and the central poorly differentiated gynoecial region of the receptacle (orthoslice xy1160); c) Flower in transverse section at the level of the floral receptacle showing 30 tepals, nine of the poorly developed stamens or staminodes, and the central poorly differentiated gynoecial region of the receptacle (orthoslice xy1250). Scale bars = 250 µm (a–c). in Multiparted, Apocarpous Flowers From The Early Cretaceous Of Eastern North America And Portugal
Text-fig. 4. Synchrotron radiation X-ray tomographic microscopy orthoslices of flowers of Lambertiflora virginiense gen. et sp. nov. from the Early Cretaceous Puddledock locality, Virginia, USA (holotype, PP53796, Puddledock sample 081). White dots – tepals, yellow dots – stamens or staminodes, red dot – central conical gynoecial region. a) Flower in longitudinal section showing elongated overlapping tepals, remains of probable poorly developed stamens or staminodes and probable poorly developed carpels on the central conical gynoecial region of the receptacle (orthoslice yz0454); b) Flower in transverse section showing rhomboidal bases of 30 tepals, nine poorly developed stamens or staminodes, and the central poorly differentiated gynoecial region of the receptacle (orthoslice xy1160); c) Flower in transverse section at the level of the floral receptacle showing 30 tepals, nine of the poorly developed stamens or staminodes, and the central poorly differentiated gynoecial region of the receptacle (orthoslice xy1250). Scale bars = 250 µm (a–c).
Text-fig. 54. Scanning electron microscope (SEM; a–e, g, h) and synchrotron x-ray microscopy (SRXTM; f, i) images of unnamed angiosperm fruits and seeds; Torres Vedras locality, Portugal. a) Follicle sp. 1, narrow elongate follicle with sessile and decurrent stigma; b) Follicle sp. 2, broad, dehisced follicle with elongate and transverse fibers lining the locule; c) Angiosperm seed sp. 1 with thin, smooth seed coat; d) Angiosperm seed sp. 2 with verrucate seed coat; e) Angiosperm seed sp. 3 with exotestal and foveolate seed coat; f) Angiosperm seed sp. 4 with smooth seed coat; g, h) Angiosperm seed sp. 5 with raised epidermal cells forming a reticulate pattern; i) Wedge-shaped angiosperm fruit with remains of floral parts near apex. Specimens, TV43-S136726 (a), TV44-S148144 (b), TV43-S170074 (c), TV43-S136747 (d), TV43-S170073 (e), TV38-S174615 (f), TV44-S148003 (g), TV44-S148004 (h), TV43-S174685 (i). Scale bars 300 Μm (a–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. 54. Scanning electron microscope (SEM; a–e, g, h) and synchrotron x-ray microscopy (SRXTM; f, i) images of unnamed angiosperm fruits and seeds; Torres Vedras locality, Portugal. a) Follicle sp. 1, narrow elongate follicle with sessile and decurrent stigma; b) Follicle sp. 2, broad, dehisced follicle with elongate and transverse fibers lining the locule; c) Angiosperm seed sp. 1 with thin, smooth seed coat; d) Angiosperm seed sp. 2 with verrucate seed coat; e) Angiosperm seed sp. 3 with exotestal and foveolate seed coat; f) Angiosperm seed sp. 4 with smooth seed coat; g, h) Angiosperm seed sp. 5 with raised epidermal cells forming a reticulate pattern; i) Wedge-shaped angiosperm fruit with remains of floral parts near apex. Specimens, TV43-S136726 (a), TV44-S148144 (b), TV43-S170074 (c), TV43-S136747 (d), TV43-S170073 (e), TV38-S174615 (f), TV44-S148003 (g), TV44-S148004 (h), TV43-S174685 (i). Scale bars 300 Μm (a–i).
Text-fig. 50. Scanning electron microscope (SEM) and synchrotron radiation X-ray tomographic microscopy (SRXTM) images of a flower and mature carpels of Reyanthus lusitanicus gen. et sp. nov.; Torres Vedras locality, Portugal. a) Holotype; multicarpellate flower showing numerous carpels surrounded by remains of the androecium and perianth; note the bract subtending the flower (arrowhead); b, c) Longitudinal sections perpendicular to section in (f) (b, SRXTM orthoslice xz0461) and (c, SRXTM cut voltex xz0540-0580) showing receptacle, carpels and remains of the androecium and perianth; note prominent cavities formed by the oil cells, subtending bract (arrow) and bract subtending fragmentary bud (arrowhead); d, e) Apical (d) and lateral (e) views of gynoecium showing laterally flattened carpels and dorsi-ventrally flattened stamen or staminode (* in e); f) Longitudinal section (SRXTM orthoslice yz0405) of gynoecium showing conical receptacle and carpels with densely spaced oil cells; g, h) Mature carpel of Reyanthus lusitanicus gen. et sp. nov. showing slightly curved form, rounded apex and base that tapers toward the attachment to the receptacle; i) Surface of carpel showing embedded oil cells; j) Transverse section through three carpels showing attachment of developing ovules near the ventral sutures and oil cells in the wall just below the surface (SRXTM cut voltex xy0770-0845). Specimens TV299-S136716 (holotype; a–f), TV299-S136717 (g–j). Scale bars 300 Μm (a–d, f–h), 150 Μm (e, j), 30 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. 50. Scanning electron microscope (SEM) and synchrotron radiation X-ray tomographic microscopy (SRXTM) images of a flower and mature carpels of Reyanthus lusitanicus gen. et sp. nov.; Torres Vedras locality, Portugal. a) Holotype; multicarpellate flower showing numerous carpels surrounded by remains of the androecium and perianth; note the bract subtending the flower (arrowhead); b, c) Longitudinal sections perpendicular to section in (f) (b, SRXTM orthoslice xz0461) and (c, SRXTM cut voltex xz0540-0580) showing receptacle, carpels and remains of the androecium and perianth; note prominent cavities formed by the oil cells, subtending bract (arrow) and bract subtending fragmentary bud (arrowhead); d, e) Apical (d) and lateral (e) views of gynoecium showing laterally flattened carpels and dorsi-ventrally flattened stamen or staminode (* in e); f) Longitudinal section (SRXTM orthoslice yz0405) of gynoecium showing conical receptacle and carpels with densely spaced oil cells; g, h) Mature carpel of Reyanthus lusitanicus gen. et sp. nov. showing slightly curved form, rounded apex and base that tapers toward the attachment to the receptacle; i) Surface of carpel showing embedded oil cells; j) Transverse section through three carpels showing attachment of developing ovules near the ventral sutures and oil cells in the wall just below the surface (SRXTM cut voltex xy0770-0845). Specimens TV299-S136716 (holotype; a–f), TV299-S136717 (g–j). Scale bars 300 Μm (a–d, f–h), 150 Μm (e, j), 30 Μm (i).
Text-fig. 49. Scanning electron microscope (SEM) and synchrotron radiation X-ray tomographic microscopy (SRXTM) images of Vedresia elliptica gen. et sp. nov. (a–c) and a multicarpellate fruit of Choffaticarpus compactus gen. et sp. nov. and associated pollen (d–j); Torres Vedras locality, Portugal. a) Holotype; small fruit showing apical stigmatic region with attached pollen; b) Group of pollen grains from the stigmatic surface of the fruit in (a) showing the long colpus and reticulate tectum; c) Pollen grains from the stigmatic surface showing the long colpus and well developed reticulum, with smooth muri and short columellae 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. 49. Scanning electron microscope (SEM) and synchrotron radiation X-ray tomographic microscopy (SRXTM) images of Vedresia elliptica gen. et sp. nov. (a–c) and a multicarpellate fruit of Choffaticarpus compactus gen. et sp. nov. and associated pollen (d–j); Torres Vedras locality, Portugal. a) Holotype; small fruit showing apical stigmatic region with attached pollen; b) Group of pollen grains from the stigmatic surface of the fruit in (a) showing the long colpus and reticulate tectum; c) Pollen grains from the stigmatic surface showing the long colpus and well developed reticulum, with smooth muri and short columellae
Text-fig. 24. Scanning electron microscope (SEM) images (a, c, d) and synchrotron radiation X-ray tomographic microscopy (SRXTM) images (b, e) of fruits and seeds of Serialis antiqua (a, b) and Serialis parva (c–e); Torres Vedras locality, Portugal. a, b) Serialis antiqua lateral view of fruit showing smooth partly abraded fruit wall (a) and longitudinal section (b, SRXTM orthoslice yz0862) showing six closely adhering seeds, some of which are mature with well-preserved nutritive tissue; c–e) Serialis parva lateral view of fruit showing faint ribs (c), finely pitted seed surface with undulate anticlinal walls of the exotestal cells (d), and transverse section showing two closely adhering seeds (SRXTM orthoslice xy0913, e). Specimens, TV43-S174480 (a, b), TV43-S170076 (c), TV43-S170079 (d), TV43-S174477 (e). Scale bars 300 Μm (a–c, e), 50 Μm (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. 24. Scanning electron microscope (SEM) images (a, c, d) and synchrotron radiation X-ray tomographic microscopy (SRXTM) images (b, e) of fruits and seeds of Serialis antiqua (a, b) and Serialis parva (c–e); Torres Vedras locality, Portugal. a, b) Serialis antiqua lateral view of fruit showing smooth partly abraded fruit wall (a) and longitudinal section (b, SRXTM orthoslice yz0862) showing six closely adhering seeds, some of which are mature with well-preserved nutritive tissue; c–e) Serialis parva lateral view of fruit showing faint ribs (c), finely pitted seed surface with undulate anticlinal walls of the exotestal cells (d), and transverse section showing two closely adhering seeds (SRXTM orthoslice xy0913, e). Specimens, TV43-S174480 (a, b), TV43-S170076 (c), TV43-S170079 (d), TV43-S174477 (e). Scale bars 300 Μm (a–c, e), 50 Μm (d).
Text-fig. 19. Scanning electron microscope (SEM; d, e) and synchrotron radiation X-ray tomographic microscopy (SRXTM; a–c) images of a seed of Kvacekispermum costatum sp. nov. (a–c) and Kvacekispermum sp. (d, e); Torres Vedras locality, Portugal. a, b) Isolated, abraded seeds showing densely spaced longitudinal ridges; c) Detail of abraded seed in (b) showing surface of endotesta with imprints of crystals; d) Isolated, abraded seed showing longitudinal ridges; e) Abraded seed surface showing surface of endotesta with imprints of crystals. Specimens, TV44-S174098 (holotype; a), TV38-S174099 (b, c), TV43-S174612 (d, e). Scale bars 300 Μm (a, b, d), 50 Μm (c, 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. 19. Scanning electron microscope (SEM; d, e) and synchrotron radiation X-ray tomographic microscopy (SRXTM; a–c) images of a seed of Kvacekispermum costatum sp. nov. (a–c) and Kvacekispermum sp. (d, e); Torres Vedras locality, Portugal. a, b) Isolated, abraded seeds showing densely spaced longitudinal ridges; c) Detail of abraded seed in (b) showing surface of endotesta with imprints of crystals; d) Isolated, abraded seed showing longitudinal ridges; e) Abraded seed surface showing surface of endotesta with imprints of crystals. Specimens, TV44-S174098 (holotype; a), TV38-S174099 (b, c), TV43-S174612 (d, e). Scale bars 300 Μm (a, b, d), 50 Μm (c, e).
Text-fig. 17. Scanning electron microscope (SEM) and synchrotron radiation X-ray tomographic microscopy (SRXTM) images of a fruit of Canrightia elongata sp. nov. (a–g) and isolated Canrightia-like seeds (h–j); Torres Vedras locality, Portugal. a–c) Holotype; fruit in lateral view showing four fused tepals at the base (c, upper arrowheads) and prominent cavities in the fruit wall formed by scattered oil bodies and possible subtending bract (c, lower arrowhead); d) Transverse section (SRXTM orthoslice xy1510) through the fruit showing three locules, one with the remains of the endothelium (top left, 1), the other two (2, 3) with remains of presumed endosperm tissue; note that the locule to the right (3) is crushed; e, f) Radial longitudinal (e; SRXTM orthoslice xz1212) 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. 17. Scanning electron microscope (SEM) and synchrotron radiation X-ray tomographic microscopy (SRXTM) images of a fruit of Canrightia elongata sp. nov. (a–g) and isolated Canrightia-like seeds (h–j); Torres Vedras locality, Portugal. a–c) Holotype; fruit in lateral view showing four fused tepals at the base (c, upper arrowheads) and prominent cavities in the fruit wall formed by scattered oil bodies and possible subtending bract (c, lower arrowhead); d) Transverse section (SRXTM orthoslice xy1510) through the fruit showing three locules, one with the remains of the endothelium (top left, 1), the other two (2, 3) with remains of presumed endosperm tissue; note that the locule to the right (3) is crushed; e, f) Radial longitudinal (e; SRXTM orthoslice xz1212)
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.