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3,465 results for “Embryo”
102 hpf medaka embryos in 96 well plate (4 embryo/well) - brightfield - 2X magnification - ACQUIFER Imaging Machine
<p>Dataset originates from:</p> <p>Gierten, J., Pylatiuk, C., Hammouda, O. T., Schock, C., Stegmaier, J., Wittbrodt, J., Gehrig, J. and Loosli, F. (2020). <strong>Automated high-throughput heartbeat quantification in medaka and zebrafish embryos under physiological conditions</strong>. Sci Rep <em>10</em>, 2046, doi:<a href="https://doi.org/10.1038/s41598-020-58563-w">10.1038/s41598-020-58563-w</a>.</p> <p>Used as benchmark dataset for Multi-Template-Matching by Thomas and Gehrig </p> <p>See implementation in Fiji <a href="https://github.com/LauLauThom/MultipleTemplateMatching">https://github.com/LauLauThom/MultipleTemplateMatching</a></p> <p>and in KNIME <a href="https://github.com/LauLauThom/MultipleTemplateMatching-KNIME">https://github.com/LauLauThom/MultipleTemplateMatching-KNIME</a></p> <p>Contacts: j.gehrig(at)acquifer.de, l.thomas(at)acquifer.de, jakob.gierten(at)cos.uni-heidelberg.de</p>
Multiplexed DNA-FISH imaging dataset, drosophila embryos, nuclear cycles 11-14
<p>Multiplexed DNA-FISH imaging dataset from Drosophila embryos at nuclear cycles 11-14.</p> <p>Examples on how to load and use this dataset can be found at this <a href="https://github.com/NollmannLab/Goetz_etal">GitHub repository</a>.</p> <p><strong>Data processing details</strong></p> <p>Barcodes were segmented using a neural network (<a href="https://github.com/stardist/stardist"><em>stardist</em></a>) specifically trained for the detection of 3D diffraction limited spots produced by our microscope. To extract the position of the barcode with sub-pixel accuracy, a subsequent 3D Gaussian fit of the regions segmented by <em>stardist</em> was performed with Big-FISH (<a href="https://github.com/fish-quant/big-fish">https://github.com/fish-quant/big-fish</a>). Barcode localizations with intensities lower than 1.5 times that of the background were filtered out.</p> <p>Nuclei were segmented from projected DAPI images using <em><a href="https://github.com/stardist/stardist">stardist</a> </em>with a neural network trained for detection of nuclei from <em>Drosophila</em> embryos under our imaging conditions. Barcodes were then attributed to single nuclei by using the XY coordinates of the barcodes and the DAPI masks of the nuclei. Finally, pairwise distance matrices were calculated for each single nucleus.</p> <p><strong>Processed data in Figures</strong></p> <p>This new version of the dataset contains the raw data for each of the figures in the manuscript:</p> <p><strong>Associated publication</strong></p> <p><strong>Multiple parameters shape the 3D chromatin structure of single nuclei at the doc locus in </strong><em>Drosophila</em>.</p> <p>Markus Götz, Olivier Messina, Sergio Espinola, Jean-Bernard Fiche, Marcelo Nollmann</p> <p>Nature Communications (2022).</p>
ISS Mouse brain embryo - MIPPED images , all rounds all channels
<p>Repository containing the stitched, mipped and aligned images of all the cycles and channels used in the Mouse embryo ISS characterization from La Manno et al 2020 The repository contains:</p> <ul> <li>Stitched aligned and mipped images of all round and cycles for different samples (2A,2D, 6B,10B)</li> <li>A codebook with the code of every expected gene detecoded is included</li> <li>A preliminary decoding of the 4 samples included in the folder "decoded_spots"</li> <li>Information about channel order in a .txt</li> </ul>
Fluorescent Macrophages in Drosophila Embryo
<p>This is a data set that contains a time sequence of<strong> fluorescently labelled macrophages</strong> that migrated in a<strong> drosophila embryo</strong>.</p> <p>The macrophages were visualised in the embryo by using the UAS/GAL4 system.We used the srpHemo-Gal4driver,which mediate the expression of genes downstream of a UASsequence specifically in macrophages to express the following UAS fluorescent probes: UAS-RedStinger for the nuclei and UAS-Clip-GFP for the microtubules.</p> <p>Details of the imaging and preparation have been published in:</p> <p> </p> <ul> <li>Evans, I.R.; Zanet, J.; Wood, W.; Stramer, B.M.<em> Live imaging of Drosophila melanogaster embryonic339hemocyte migrations.Journal of visualized experiments:</em> JoVE2010,36.</li> </ul> <p> </p> <p>Details on the segmentation, tracking and analysis of the macrophage migration have been published in:</p> <ul> <li>José Alonso Solís-Lemus, Besaiz J Sánchez-Sánchez, Stefania Marcotti, Mubarik Burki, Brian Stramer, Constantino Carlos Reyes-Aldasoro, <em>Comparative study of contact repulsion in control andmutant macrophages using a novel interaction detection</em>, Journal of Imaging, BioRxiv, https://doi.org/10.1101/2020.03.31.018267</li> </ul> <p>and</p> <ul> <li>Solís-Lemus, J.A.; Stramer, B.; Slabaugh, G.; Reyes-Aldasoro, C.C. <em>Macrosight: A Novel Framework to Analyze the Shape and Movement of Interacting Macrophages Using Matlab</em>.Journal of Imaging 2019,5</li> </ul> <p> </p>
Four angle fused dataset for Ascidian embryo imaged via light sheet
<p>Original dataset imaged and published here: </p> <pre>DOI: 10.6084/m9.figshare.8235473.v1</pre> <p>This dataset is provided as Raw dataset for training deep neural networks for segmentation tasks. The binary masks and the integer labels are provided separately.</p>
Gene-level counts according to their poly(A) length and additional uridine modifications in several stages of zebrafish, Xenopus, and mouse embryos
<p>This HDF5 file contains the processed data of primary poly(A) tail length analyses for the TAIL-seq runs used for Chang and Yeo et al. (2018; doi:10.1016/j.molcel.2018.03.004). The read count tables are stored under the two-level group structure of the run identifier as the first level and the sample identifier as the second level. A dataset at a leaf node is an unsigned integer array of the read count numbers by the length of poly(A) in rows and the length of U tails following after poly(A) in columns.</p> <p>Please refer to the <a href="https://data.mendeley.com/datasets/tzc5wwczyg/1">supplementary data page</a> of the original paper for more information about the experimental design.</p> <p> </p>
Embryo and larval biology of the deep-sea octocoral Dentomuricea aff. meteor
<p>The study focuses on the early life stages of the species <em>Dentomuricea</em> aff. <em>meteor</em>, a common deep-sea octocoral in the Azores. The objective was to describe the embryo and larval development, survival and swimming behaviour of early life stages of the target species, under two temperature regimes, corresponding to the minimum and maximum temperatures in its natural environment during the spawning season (13 °C and 15°C). Embryo and larval development were monitored closely and revealed faster developmental rates under 15°C . Survival counts were performed throughout embryo and larval development, but were not statistically different between temperatures. Moreover, swimming behaviour was assessed by means of video recordings, revealing a higher larval swimming speed at 15°C. Additional data on larval behaviour are provided, including settlement and metamorphosis rates which were low for both temperatures. Our results showcase how small temperature fluctuations can affect embryo and larval characteristics, potentially impacting larval dispersal and success.</p>
Stardist model for Ascaidan embryo
<p>Stardist trained model for doing object detection of membrane labelled Ascadian mouse embryo cells.</p>
Data for: Heat induces multiomic and phenotypic stress propagation in zebrafish embryos
<p>This contains the data for the manuscript Feugere et al., "Heat induces multiomic and phenotypic stress propagation in zebrafish embryos" (2023). Zebrafish embryos were exposed to thermal stress ("TS") and stress metabolites ("SM") released by heat-stressed conspecifics in a two-way factorial design ("TSxSM"). The folder includes raw molecular data (cortisol levels, HSP70 protein levels, and gene expression acquired with LAMP and RNA-seq) and raw phenotypic data (morphology, hatching, survival, and behaviour) of zebrafish <em>Danio rerio </em>at 1 day and 4 days of development.</p> <p>The .csv files contain all quantitative data, whilst the .tab files contain the gene count data required for gene expression analysis. The data were analysed in R using the code shared in the "TSxSM2.stats.Rmd" file. The "Metadata" document provides the reader with an extensive description of each file.</p>
Early Embryo DNA Data and Code
<p>CODE FOR ANALYSIS PRESENTED IN "INCLUDING THE INVISIBLE FRACTION IN WHOLE POPULATION STUDIES: A GUIDE TO THE GENETIC SAMPLE OF UNHATCHED BIRD EGGS" - FAY MORLAND, SELINA PATEL, ANNA SANTURE, PATRICIA BREKKE, NICOLA HEMMINGS</p><p>CONTACT FAY MORLAND FAY.MORLAND@OTAGO.AC.NZ WITH ANY QUERIES </p>
Whole mouse embryo microCT image with nuclear staining (Bleikern)
<p>E12.5 mouse embryo stained with lead(II) acetate to contrast cell nuclei. X-ray microtomography scan as TIFF stack, 2.5um voxel size. Data used in publication</p> <p>Metscher B. (2021). A simple nuclear contrast staining method for microCT-based 3D histology using lead(II) acetate. Journal of Anatomy 238(4): 1036-1041.<br> https://onlinelibrary.wiley.com/doi/10.1111/joa.13351</p> <p> </p>
Supplementary data for calcium-vesicles perform active diffusion in the sea urchin embryo during larval biomineralization
<p><strong>Supplementary datasets for the paper Calcium-vesicles perform active diffusion in the sea urchin embryo during larval biomineralization.</strong></p> <p>Two deskewed and deconvolved lattice light-sheet datasets (100 frames each) from the live-cell experiments are available, a control embryo dataset (01-07-2016_TimeLapse4_DMSO_21hrs_Calcein_FM464) and a VEGFR inhibited dataset (24-06-2016_Timelapse1_Axtinib_150_19hrs_Calcein_FM464). These datasets were used for collecting size and motion statistics. The control embryo dataset is available in raw microscope output without deskew or deconvolution applied (Raw_01-07-2016_TimeLapse4_DMSO_21hrs_Calcein_FM464).</p> <p>Four confocal datasets from the cytoskeletal remodeling experiments are also included, phalloidin stained images, control (Phalloidin PMC DMSO 5 zoom4s) and VEGFR inhibited (Phalloidin PMC Axt 18 zoom4); and myosinIIP stained images, control (Myosin PMC 30h DMSO new slid 4a zoom4) and VEGFR inhibited (Phalloidin PMC Axt 18 zoom4).</p> <p>Source code and instructions for the analysis tools used for both the lattice light-sheet and confocal data is available at: <a href="https://git-bioimage.coe.drexel.edu/opensource/llsm-calcium-vesicles-lever">https://git-bioimage.coe.drexel.edu/opensource/llsm-calcium-vesicles-lever</a></p> <p>Code for the deconvolution and deskew algorithms is available from the Janelia research center at: <a href="https://www.janelia.org/open-science/lattice-light-deconvolution-software-cudadeconv">https://www.janelia.org/open-science/lattice-light-deconvolution-software-cudadeconv</a></p> <p> </p> <p> </p>
Density analysis of lymph node anlagen in whole mount acquired mouse embryos
<p>Raw data and script permitting to analyse the density of cervical, mandibular and axillary lymph node anlagen in whole mount aquired mouse embryos.</p>
Danio rerio (Cyprinidae) - whole organism - embryo
Image of Danio rerio (Cyprinidae) - whole organism - embryo
Danio rerio (Cyprinidae) - whole organism - embryo
Image of Danio rerio (Cyprinidae) - whole organism - embryo
Danio rerio (Cyprinidae) - whole organism - embryo
Image of Danio rerio (Cyprinidae) - whole organism - embryo
Danio rerio (Cyprinidae) - whole organism - embryo
Image of Danio rerio (Cyprinidae) - whole organism - embryo
Danio rerio (Cyprinidae) - whole organism - embryo
Image of Danio rerio (Cyprinidae) - whole organism - embryo
Danio rerio (Cyprinidae) - whole organism - embryo
Image of Danio rerio (Cyprinidae) - whole organism - embryo
Danio rerio (Cyprinidae) - whole organism - embryo
Image of Danio rerio (Cyprinidae) - whole organism - embryo
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)
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.