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42 results for “serial sectioning”
Platynereis dumerilii - Aligned serial sections of the posterior segments
<p>Aligned serial semi-thin sections (1µm) of the posterior most segments of <em>Platynereis dumerilii.</em></p>
Capillary networks and follicular marginal zones in the human spleen. Three-dimensional models based on immunostained serial sections - Supplementary videos
<p>We regard ROIs, regions of interest, from a human spleen specimen in single (four ROIs) and double (three ROIs) staining. The ROIs with the same number correspond to each other. Below we map references in manuscript (<strong>bold</strong>) to file names in this repository (<em>italics</em>).</p> <ul> <li>File <em>colour-deconvolution.png</em> – settings of colour deconvolution in Fiji for double staining.</li> <li>File <em>comments to videos.odt</em> – a commentary to S3[c,d] Video.</li> <li><strong>S1a,b Video to S3a,b Video</strong>: files <em>video_[1,2,3][a,b].mov</em> – sequence of section with single (a) and double (b) staining for ROI 1 to 3 in the main text.</li> <li><strong>S1c Video to S3c Video</strong>: files <em>video_[1,2,3]c.mov</em> – video of the reconstruction, single staining, special blood vessels highlighted.</li> <li><strong>S1d Video to S4d Video</strong>: files <em>video_[1,2,3]d.mov</em> – an overview video of the reconstruction, double staining.</li> <li><strong>S4 Video</strong>: file <em>video_4.mov</em> – quality control in virtual reality.</li> <li><strong>S1 Figure</strong>: a supplementary figure <em>fig_S1.tiff</em> and its caption <em>fig_S1_legend.odt</em></li> <li><strong>S2 Figure</strong>: a supplementary figure <em>fig_S2.tiff</em> and its caption <em>fig_S2_legend.odt</em></li> </ul> <p>This data corresponds to the publication "Capillary networks and follicular marginal zones in the human spleen. Three-dimensional models based on immunostained serial sections" by B. S. Steiniger, C. Ulrich, M. Berthold, M. Guthe, and O. Lobachev, 2017.</p>
Evaluating registrations of serial sections with distortions of the ground truths. Supplemental data
<p><strong>Evaluating Registrations of Serial Sections With Distortions of the Ground Truths</strong></p> <p>This is the supplemental data for our paper on how to benchmark registrations of serial sections with ground truths. The files are named as follows:</p> <ul> <li>*_challenge.7z: local distortions and global rigid transformations applied, the input for the benchmark we used. Use this to test your rigid and non-rigid methods.</li> <li>*_local-only.7z: only local distortions applied.</li> <li>*_local-DIST.7z: the distortion maps for local distortions.</li> <li>*_SURF-rigid.7z: local distortions and global rigid transformations applied, rigid transformations undone with SURF-based rigid-only method. Local distortions remain. Use this if your method does not cope well with large rigid transformations.</li> <li>_*vis.7z: visualizations of distortions.</li> <li>_rigid_ground.7z: the real rigid transformations used in the global phase.</li> <li>*_ground.7z: the ground truth. All data fit each other, no distortions. Use this to compare your registration result to it.</li> </ul> <p>There are three main modalities and one further, as a reference:</p> <ul> <li>CT_*: µCT data, a rabbit lung, 600 images. (In ground truth, and local distortions, and global transformations we supply more images that went into the benchmark, 50 more from both beginning and end.)</li> <li>EM_*: an EM serial block-face (SBF-SEM) data set of adult mouse lung, 1000 images. (EM ground truth is individually normalized, see paper.)</li> <li>LS_*: a lung from the light sheet microscopy from a male 24 week-old rat, 300 images. (LS ground truth is individually normalized, too.)</li> <li>REAL_*: a region from real serial sections from a rabbit lung, 2 images.</li> </ul> <p>We also supply elastix parameter files.</p> <p>A preprint has been uploaded to <a href="https://arxiv.org/abs/2011.11060">arXiv</a>. The definite version is available from <a href="https://ieeexplore.ieee.org/abstract/document/9594850/media#media">IEEE</a>. The source code of the distorter is available from <a href="https://github.com/olegl/distort">GitHub</a>.</p>
Feature-based multi-resolution registration of immunostained serial sections - online material
<p>This is the supplementary online material, including full data, evaluation, and executables, for the paper "Feature-based multi-resolution registration of immunostained serial sections" that appeared in Medical Image Analysis, Volume 35, January 2017, Pages 288–302.</p> <p>Same material was deposited online under https://gdv-server.inf.uni-bayreuth.de/gdvcloud/index.php/s/NnSov0O65n9Gp01 </p> <p>We also include here further supplementary files deposited at the journal page (http://www.sciencedirect.com/science/article/pii/S136184151630127X) under CC-BY licence. See there for the definite version of the paper or http://www.mathematik.uni-marburg.de/~lobachev/papers/lobachev-media16-registration-preprint.pdf for the preprint.</p>
FIG. 5. — Serial cross sections from below upwards through a in Comparative floral anatomy of some species of Brassicaceae and its taxonomic significance
FIG. 5. — Serial cross sections from below upwards through a floral bud of Matthiola incana (L.) R.Br. showing: A, pedicel vasculature; continuous siphonostele; B-F, calyx vasculature; two sepal median bundles emerge directly from central stele and two from sepal-median-nectarial complexes; D-G, corolla vasculature; from petal-sepal marginal complexs; D-H, androecium vasculature; six staminal bundles to six fertile stamens emerge directly from the central stele; I-L, gynoecium vasculature, eight vascular masses; two dorsal carpellary bundles, two ventral carpellary masses, four lateral carpellary bundles. Scale bar: 500 μm.
FIG. 3. — Serial cross sections from below upwards through a in Comparative floral anatomy of some species of Brassicaceae and its taxonomic significance
FIG. 3. — Serial cross sections from below upwards through a floral bud of Coronopus didymus (L.) Sm. showing: A, pedicel vasculature; dissected siphonostele; B-D, calyx vasculature; four sepal median bundles arise directly from the central stele as distinct sepal median traces without ramification; C-E, corolla vasculature; four petal vascular bundles protrude from petal-nectarial complexes; C-G, androecium vasculature; two staminal vascular bundles to two fertile stamens emerge directly from the central stele; F-K, gynoecium vasculature; six vascular masses, two dorsal carpellary bundles, two ventral carpellary masses, two septal bundles. Scale bar: 60 μm.
FIG. 1. — Serial cross sections from below upwards through a in Comparative floral anatomy of some species of Brassicaceae and its taxonomic significance
FIG. 1. — Serial cross sections from below upwards through a floral bud of Brassica nigra (L.) W.D.J.Koch showing: A, pedicel vasculature; continuous siphonostele; B-F, Calyx vasculature; two sepal median bundles emerge directly from central stele and two from sepal-median-nectarial complexes; D-F, corolla vasculature; from petal-sepal marginal-nectarial complexes; D-G, androecium vasculature; the two outer stamens receive the vascular supply from two staminal-nectarial complexes while the four inner receive directly from the central stele; I-M, gynoecium vasculature; ten vascular masses; two dorsal carpellary bundles, two ventral carpellary masses, four lateral carpellary bundles and two septal bundles. Scale bar: 200 μm.
FIG. 2. — Serial cross sections from below upwards through a in Comparative floral anatomy of some species of Brassicaceae and its taxonomic significance
FIG. 2. — Serial cross sections from below upwards through a floral bud of Raphanus sativus L. showing: A, pedicel vasculature; dissected siphonostele; B-F, calyx vasculature; four sepal median bundles arise directly from the central stele as distinct sepal median traces, two antero-posterior ramified and two laterals unramified; C-E, corolla vasculature; from petal-sepal marginal complexes; D-I, androecium vasculature; six staminal bundles to six fertile stamens emerge directly from the central stele; J-N, gynoecium vasculature; ten vascular masses; two dorsal carpellary bundles, two ventral carpellary masses, four lateral carpellary bundles and two septal bundles. Scale bar: 500 μm.
Serial Coronal Sections Of An Adult Mouse Brain - Sample Dataset
<p>Experimental data: 88 serial coronal sections of the full brain of an adult mouse.</p> <p>Preparation of the sample: details to come...</p> <p>Imaging of the sample: details to come...</p> <p>2 channels per section are present:</p> <ul> <li>DAPI</li> <li>autofluorescence</li> </ul> <p>This dataset is used in particular as a test dataset for the <a href="https://c4science.ch/w/bioimaging_and_optics_platform_biop/image-processing/image-to-atlas-registration/">Allen Brain Biop Aligner Fiji plugin</a>.</p> <p>Some sections are flipped (left / right), for workflow documentation purpose.</p> <p>Animal handling according to protocols approved by the Swiss animal license VD2808.1</p>
Platynereis dumerilii - Aligned serial sections of the parapodium used for the 3D Model
<p>Aligned serial semi-thin sections (1µm) of a parapodium of <em>Platynereis dumerillii. </em></p>
Whole slide images of mouse liver serial sections - Test registration dataset
<p>15 H&E serial section of mouse liver and small intestine.</p> <p>Sampled prepared in the <a href="https://www.epfl.ch/research/facilities/histology-core-facility/">EPFL histology core facility</a> by Nathalie Müller, Gian-Filippo Mancini, and Agnès Hautier.</p> <p>All slides where imaged with a VS200 Evident slide scanner from the<a href="http://biop.epfl.ch/"> EPFL BIOP imaging facility</a>.</p>
FIGURE 28. Cheiracanthus latus pectoral spines, serial transverse section drawings. 1, NMS G.2018.28.26 in A redescription of the three longest-known species of the acanthodian Cheiracanthus from the Middle Devonian of Scotland
FIGURE 28. Cheiracanthus latus pectoral spines, serial transverse section drawings. 1, NMS G.2018.28.26 (see Figure 27): sketch map and drawings of each section. 2, NMS G.2019.3.7 (see Figure 6.7, 8): sections NMS G.2019.3.7.6-12 through pectoral spines and scapulocoracoid.
Cross-sectional serial block-face images of rat tail tendon fascicle
<p>Cross-sectional serial block-face images of rat tail tendon fascicles</p> <p>resolution: 10nm x 10nm x 200nm</p> <p>432 slices</p> <p>Copyright Babak N. Safa - Elliott Lab University of Delaware 2019</p>
FIGURE 7 in Picking up the pieces: the digital reconstruction of a destroyed holotype from its serial section drawings
FIGURE 7. The state of preservation of the wax model of BP/1/1821. 1, the right side of the snout showing the deformation of the canine; 2, the palate showing the broken vomer; 3, the basicranium showing multiple cracks, nails and sticks around the pterygoid; 4, view of the right orbit showing multiple cracks, nails and sticks; 5, dorsal view of the of the mandible showing multiple cracks, nails and sticks; 6, detail of the inner side of the left ascending ramus of the mandible showing a stick embedded in the wax; and 7, lateral view of the mandible showing the incomplete reflected lamina of the angular. The arrows point to the nails, dotted lines demarcate the cracks. Not to scale.
FIGURE 6 in Picking up the pieces: the digital reconstruction of a destroyed holotype from its serial section drawings
FIGURE 6. Comparison between the digital model (top) and the wax model (bottom), in rostral (left) and lateral views (right). Arrows indicate the direction of deformation of the wax model. Scale bar equals 10 mm.
FIGURE 5 in Picking up the pieces: the digital reconstruction of a destroyed holotype from its serial section drawings
FIGURE 5. Segmentation of the skull bones of BP/1/1821, (1) in the cranium and (2) in the lower jaw. Scale bar equals 10 mm.
FIGURE 4 in Picking up the pieces: the digital reconstruction of a destroyed holotype from its serial section drawings
FIGURE 4. The slices of specimen BP/1/1821 finally put back together again, as seen in the hands of the CT scan facility technician K. Jakata (ESI). This 3D printed model is the first time in 55 years that BP/1/1821 has been accurately reconstructed at life-size.
FIGURE 3 in Picking up the pieces: the digital reconstruction of a destroyed holotype from its serial section drawings
FIGURE 3. The digital model in (1) right lateral, (2) left lateral and (3) ventral view in stereopairs. Scale bar equals 10 mm. See also the supplementary video in Appendix 2.
FIGURE 2 in Picking up the pieces: the digital reconstruction of a destroyed holotype from its serial section drawings
FIGURE 2. Comparison of the different reconstructions of BP/1/1821 in dorsal (left) and ventral (right) views. 1, the wax model; and 2, the original illustrations by Brink, found with the serial section drawings.
FIGURE 1 in Picking up the pieces: the digital reconstruction of a destroyed holotype from its serial section drawings
FIGURE 1. The label on the first page of the serial section drawings. It is written "Specimen N°1821 (FN). MN° 346. Complete Aneumogomphius? skull therocephalian. Sections ½ mm. Magnification x4." The document is signed "A.S. Brink". Abbreviations: FN, Field Number; MN°, Museum Number.
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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.