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3 results for “Hybrid annotation”
MicroCT scans of a hybrid poplar leaf dehydrating, with annotated slices for model training
<p>Dataset of a leaf segment of a hybrid poplar (<em>P. maximowiczii x P. nigra</em> ‘Max3’) leaf scanned using microcomputed tomography (microCT) over time as it dehydrates.</p> <p> </p> <p><strong>Data acquisition methodology</strong></p> <p>Plants were brought to the TOMCAT tomographic beamline of the Swiss Light Source at the Paul Scherrer Institute (Villigen, Switzerland). Before microCT scanning, a young fully expanded leaf was detached from the plant and a short strip (0.4 x 1.5 cm) was cut between second-order veins. The base of the strip was wrapped in polyimide tape and inserted into a styrofoam block fixed on a sample holder. The strip was immediately scanned by imaging 1801 projections of 100 ms under a beam energy of 21 keV and a magnification of 40x, yielding a final voxel size of 0.1625 µm (field of view: ~416x416x312 µm). The leaf was left to dehydrate in the holder and additional scans were taken 10, 20, 25, and 30 minutes after the initial scan. Scanned projections were reconstructed to a transverse view using both absorption (gridrec; Marone <em>et al.</em> 2012) and phase contrast enhancement (Paganin <em>et al.</em> 2002) reconstruction.</p> <p> </p> <p><strong>Dataset description</strong></p> <p>On the reconstructed images a region of interest was identified using a paradermal view (i.e. top to bottom of the leaf) and used to manually align the scans of each time step. Thereafter, all images were cropped to that ROI, ensuring that the same region of the leaf was present in all image stacks.</p> <p>For all stacks, files start with:<br> <em>DEHYDRATION_small_Leaf4_time_N_</em><br> where N is the time point, with values from 1 to 5 equaling 0, 10, 20, 25, and 30 minutes.</p> <p>Following this prefix is either GRID (gridrec reconstruction), PAGANIN (phase contrast enhancement reconstruction), or LABELLED (hand labelled slices or ground truth). For GRID and PAGANIN, 8-bit grayscale stacks are provided. The AOI suffix indicates the region of interest.</p> <p>Stacks have been hand labelled over three orientations (for visual examples of the orientations see <a href="https://zenodo.org/api/files/6f06d15b-3ee9-412d-82ca-a20336c4bffa/Labeled_Sections_order_time1.png?versionId=26fc15aa-702e-4052-b162-702cc567634c">Labeled_Sections_order_time1.png</a> and <a href="https://zenodo.org/api/files/6f06d15b-3ee9-412d-82ca-a20336c4bffa/Labeled_Sections_order_time2.png">Labeled_Sections_order_time2.png</a>):</p> <ol> <li>CROSS (cross sectional, or transverse, view)</li> <li>LONGI (longitudinal view: similar to cross sectional view but starting normal to it, i.e. along the depth of the stack starting from the left of the cross-sectional view)</li> <li>PARADERMAL (top to bottom view: starting at the upper epidermis)</li> </ol> <p>A general idea of the slice range within one LABELLED stack is presented after the orientation, as:<br> <em>STARTtoENDbyRANGE</em><br> The exact position of the labelled slices for each time point can be found in the <a href="https://zenodo.org/api/files/6f06d15b-3ee9-412d-82ca-a20336c4bffa/Labeled_slices_positions.txt?versionId=93d7e22f-9f07-4f98-8c49-d93e9a2e1ce5">Labeled_slices_positions.txt </a>file. <strong>Note that one-based indexing is used (as in ImageJ), not zero-based indexing (as in e.g. Python).</strong></p> <p> </p> <p><strong>References</strong></p> <p>Marone F, Stampanoni M. 2012. Regridding reconstruction algorithm for realtime tomographic imaging. Journal of Synchrotron Radiation 19: 1029–1037.</p> <p>Paganin D, Mayo SC, Gureyev TE, Miller PR, Wilkins SW. 2002. Simultaneous phase and amplitude extraction from a single defocused image of a homogeneous object. Journal of Microscopy 206: 33–40.</p>
Assemblies and annotations from the paper "Interspecies hybridization as a route of accessory chromosome origin in fungal species infecting wild grasses"
<div> <p>This repository contains the whole genome assemblies, gene and TE annotations generated and analyzed in the manuscript entitled "Interspecies hybridization as a route of accessory chromosome origin in fungal species infecting wild grasses". </p> <p>Preprint available on BioRxiv:</p> <p>https://www.biorxiv.org/content/10.1101/2024.10.03.616481v1</p> <p> </p> </div>
FIGURE. Cumulative number of ferns and lycophytes, including varieties and hybrids, that were added to the Honduran flora since 1975 (A). Cumulative number of authors contributing to the addition of new records to the flora since 1975 (B). in Ferns and Lycophytes of Honduras: A new annotated checklist
FIGURE. Cumulative number of ferns and lycophytes, including varieties and hybrids, that were added to the Honduran flora since 1975 (A). Cumulative number of authors contributing to the addition of new records to the flora since 1975 (B).
ScienceDex guides
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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)
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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.