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.
209
datasets available to search
ShareScore release 0.9.0
Dataset results
209 results for “Confocal Microscopy”
Confocal Microscopy Imaging of Peptidoglycan Uptake in the Mouse Intestine
<p>Confocal imaging data set accompanying Fig.5 and Fig.6 for the article: Wheeler R, Dias Bastos PA, Disson O, Rifflet A, Gabanyi I, Spielbauer J, Bérard M, Lecuit M, Gomperts Boneca I. Microbiota-induced active translocation of peptidoglycan across the intestinal barrier dictates its within-host dissemination (2023) PNAS; doi: 10.1073/pnas.2209936120<br> <br> Stainings are described in detail in the the PNAS article methodology.<br> Files names beginning Fig 5A-1; DAPI, WGA, anti-E-cadherin, MDP-rhodamine<br> Files names beginning Fig 5A-2, Fig 5A-3 & Fig S5; DAPI, Phalloidin, anti-Siglec-F, MDP-rhodamine<br> Files names beginning Fig 5B; DAPI, Phalloidin, <em>E.coli </em>peptidoglycan-Alexa Fluor 647 conjugate<br> Files names beginning Fig 6B; DAPI, Phalloidin, anti-Siglec-F, MDP-rhodamine (also corresponds to Supplementary data Figure 5)<br> Files names beginning Fig S5-1; DAPI, Phalloidin, anti-CgA, MDP-rhodamine<br> Files names beginning Fig S5-2; DAPI, Phalloidin, anti-NKM-16-4-2, MDP-rhodamine</p>
Confocal microscopy images (CZI files) of human chondrocytes of different resolutions and magnifications with stained nuclei and primary cilia
<p>This dataset is an addition of https://doi.org/10.5281/zenodo.7994589. Here, we have focused on the influence of the magnifications of microscope objectives and image resolution on the results of automated cilia length measurements.</p> <p>1. Methods</p> <p>1.1 Cell culture</p> <p>Human non-degenerative chondrocytes from a 30-year-old male donor (NHAC-kn, CC-2550; LONZA, Walkersville Inc., Walkersville, MD, USA) were used. These chondrocytes were seeded in passage four with a density of 28000 cells/cm<sup>2</sup> on collagen-coated glass coverslips (GG-15-Collagen; Neuvitro Corporation, Camas, WA, USA). The cells were cultivated in 12-well plates (Thermo Fisher Scientific Inc., Waltham, MA, USA) under hypoxic conditions at 37°C, 5% CO<sub>2</sub> and 5% O<sub>2</sub> with different media compositions for three days.<br> The basal medium consisted of Dulbecco’s Modified Eagle Medium (DMEM) (Gibco™) including high glucose (GlutaMAX™), sodium pyruvate supplements (Thermo Fisher Scientific Inc., Waltham, MA, USA), as well as 1% penicillin/streptomycin (Pen/Strep; Thermo Fisher Scientific Inc.), 1% Amphotericin B (Biochrom GmbH, Berlin, Germany), and 50 µg mL<sup>−1</sup> ascorbic acid (Sigma-Aldrich, Merck KGaA, Darmstadt, Germany). To this basal medium, the following supplements were added: ITS with Dexa + IGF-1 + TGF-β1: 1% Insulin-Transferrin-Selenium (ITS+™), 100 nM dexamethasone, 50 ng mL<sup>−1</sup> insulin-like growth factor (IGF)-1 (R&D Systems, Minneapolis, MN, USA) and 50 ng mL<sup>−1</sup> transforming growth factor (TGF)-β1 (Peprotec, Hamburg, Germany).</p> <p>1.2 Immunocytochemistry</p> <p>After three days of cultivation in the different media compositions, the chondrocytes were washed once with phosphate-buffered saline (PBS; Biochrom GmbH, Berlin, Germany) and fixed for 10 min at room temperature (RT) with 4% paraformaldehyde (ROTI ® Histofix, Carl Roth GmbH + Co. KG, Karlsruhe, Germany). After fixation, cells were washed again and permeabilized with 0.2% Triton-X100 (Merck, Darmstadt, Germany) for 10 min. For blocking the unspecific binding sites, cell-seeded coverslips were incubated with bovine serum albumin (BSA; Sigma-Aldrich) with a concentration of 5% in PBS for one hour at RT after another washing step with PBS. To stain the primary cilium, cells were incubated with anti-acetylated α-tubulin (6-11B-1) (RRID: AB 628409) labeled with Alexa Fluor 647 (sc-23950 AF647, Santa Cruz Biotechnology, Dallas, TX, USA) diluted 1:200 in PBS at 4°C overnight. Additionally, the Actin cytoskeleton was stained with Acti-stain 488 Fluorescent Phalloidin (Cytoskeleton, Inc., Denver, CO, USA) diluted 10 in PBS for 30 min at RT. Afterward, cells were washed three times with PBS, and the coverslips were fixed with Fluoroshield™ (Sigma-Aldrich) containing 4’,6-Diamidino-2-phenylindole (DAPI).</p> <p>1.3 Image acquisition</p> <p>Three-dimensional fluorescence images of stained cells were acquired with a ZEISS ELYRA LSM 780 confocal laser scanning microscope (CLSM) (Carl Zeiss AG, Oberkochen, Germany). To find optimal microscopy parameters for automated detection and length measurement of primary cilia, images were recorded using a Plan-Apochromat 63×/1.40 Oil DIC M27 objective (Carl Zeiss AG, Oberkochen, Germany) or an α Plan-Apochromat 100 × /1.46 Oil DIC M27 Elyra objective (Carl Zeiss AG, Oberkochen, Germany) as well as the following resolutions: 1024 × 1024, 2048 × 2048 and 4096 × 4096 pixels resulting in different voxel sizes (see metadata of files).</p>
Confocal microscopy images (CZI files) of human chondrocytes in different cell culture media with stained nuclei and primary cilia
<p>1. Methods</p> <p>1.1 Cell culture</p> <p>For investigating the influence of the cell culture medium composition on the lengths of primary cilia, human non-degenerative chondrocytes from a 30-year-old male donor (NHAC-kn, CC-2550; LONZA, Walkersville Inc., Walkersville, MD, USA) were used. These chondrocytes were seeded in passage four with a density of 28000 cells/cm<sup>2</sup> on collagen-coated glass coverslips (GG-15-Collagen; Neuvitro Corporation, Camas, WA, USA). The cells were cultivated in 12-well plates (Thermo Fisher Scientific Inc., Waltham, MA, USA) under hypoxic conditions at 37°C, 5% CO<sub>2</sub> and 5% O<sub>2</sub> with different media compositions for three days.<br> The basal medium consisted of Dulbecco’s Modified Eagle Medium (DMEM) (Gibco™) including high glucose (GlutaMAX™), sodium pyruvate supplements (Thermo Fisher Scientific Inc., Waltham, MA, USA), as well as 1% penicillin/streptomycin (Pen/Strep; Thermo Fisher Scientific Inc.), 1% Amphotericin B (Biochrom GmbH, Berlin, Germany), and 50 µg mL<sup>−1</sup> ascorbic acid (Sigma-Aldrich, Merck KGaA, Darmstadt, Germany). To this basal medium, different supplements were added, creating four groups:<br> 1) ITS: 1% Insulin-Transferrin-Selenium (ITS+™ Premix, BD Biosciences, Franklin Lakes, NJ, USA),<br> 2) ITS with Dexa: 1% Insulin-Transferrin-Selenium (ITS+™) and 100 nM dexamethasone (Sigma-Aldrich, Merck KGaA, Darmstadt, Germany),<br> 3) ITS with Dexa + IGF-1 + TGF-β1: 1% Insulin-Transferrin-Selenium (ITS+™), 100 nM dexamethasone, 50 ng mL<sup>−1</sup> insulin-like growth factor (IGF)-1 (R&D Systems, Minneapolis, MN, USA) and 50 ng mL<sup>−1</sup> transforming growth factor (TGF)-β1 (Peprotec, Hamburg, Germany),<br> 4) FBS: 10% fetal bovine serum (FBS, Pan Biotech, Aidenbach, Germany).</p> <p>1.2 Immunocytochemistry</p> <p>After three days of cultivation in the different media compositions, the chondrocytes were washed once with phosphate-buffered saline (PBS; Biochrom GmbH, Berlin, Germany) and fixed for 10 min at room temperature (RT) with 4% paraformaldehyde (ROTI ® Histofix, Carl Roth GmbH + Co. KG, Karlsruhe, Germany). After fixation, cells were washed again and permeabilized with 0.2% Triton-X100 (Merck, Darmstadt, Germany) for 10 min. For blocking the unspecific binding sites, cell-seeded coverslips were incubated with bovine serum albumin (BSA; Sigma-Aldrich) with a concentration of 5% in PBS for one hour at RT after another washing step with PBS. To stain the primary cilium, cells were incubated with anti-acetylated α-tubulin (6-11B-1) (RRID: AB 628409) labeled with Alexa Fluor 647 (sc-23950 AF647, Santa Cruz Biotechnology, Dallas, TX, USA) diluted 1:200 in PBS at 4°C overnight. Additionally, the Actin cytoskeleton was stained with Acti-stain 488 Fluorescent Phalloidin (Cytoskeleton, Inc., Denver, CO, USA) diluted 10 in PBS for 30 min at RT. Afterward, cells were washed three times with PBS, and the coverslips were fixed with Fluoroshield™ (Sigma-Aldrich) containing 4’,6-Diamidino-2-phenylindole (DAPI).</p> <p>1.3 Image acquisition</p> <p>Three-dimensional fluorescence images of stained cells were acquired with a ZEISS ELYRA LSM 780 confocal laser scanning microscope (CLSM) (Carl Zeiss AG, Oberkochen, Germany). Images were recorded using a Plan-Apochromat 63×/1.40 Oil DIC M27 objective (Carl Zeiss AG, Oberkochen, Germany). The distance of two layers was 0.2814 µm and the resolution 1024 × 1024 pixels (scan magnification: 0.6, pixel length: 0.2196 µm).</p>
Confocal microscopy findings of K17 in OLP.
<p>Raw data of figure 7.</p>
Super-resolved Reflectance Confocal Microscopy 3D reconstruction of a Diatom shell
<p>These movies present back-to-back the performance in term of resolution of both standard reflectance confocal microscopy and super-resolved rescanned reflectance confocal microscopy. One movie is a 3D stack angular rotation, the other is a Zstack. </p> <p> </p>
Super-resolved Reflectance Confocal Microscopy data on Diatom shells and live MEF cells
<p>This dataset is linked to a paper submission in Open Research Europe. It contains the RAW data of confocal reflectance super-resolved point spread function, diatom shell zstack and time lapse imaging of a living Mouse Embryonic Fibroblast cell. </p>
Super-resolved Reflectance Confocal Microscopy time-lapse imaging of a living MEF cell lamellipod
<p>This movies presents a time-lapse of a label-free living Mouse embryonic fibroblast cell observed with super-resolved rescanned reflectance confocal microscopy.. </p>
V79 fibroblasts loaded with 50 nm PVP coated gold particles captures by confocal laser scanning microscopy
<p>Data was recorded continuously in a region of 41x41 μm² at a scan rate of 1400 Hz resulting in a frame duration of 94 ms; the pinhole was set to 600 μm (5.778 μm layer), image resolution was 256x256 pixel. (11 FPS)</p>
Dataset of confocal microscopy - Rhamnogalacturonan-II dimerization deficiency impairs the coordination between growth and adhesion maintenance in plants
<p>This contains additional data relative to version 1, corresponding to a new versio of the manuscript. </p> <p>This data set contains confocal images (3D stacks and 2D projections) from propidium iodide stained <em>Arabidopsis thaliana </em>dark grown hypocotyls of various wildtype and mutant plants reported in the study "Rhamnogalacturonan-II dimerization deficiency impairs the coordination between growth and adhesion maintenance in plants" (https://www.biorxiv.org/content/10.1101/2024.11.26.625362v1). Data was acquired following method described in the publication.</p> <p> </p>
Scan tiles obtained through Confocal Laser Scanning Microscopy for roughness characterization of surfaces
<p>The Data includes all the original data collected from individual scan tiles of both quartz and glass surfaces using Confocal Laser Scanning Microscopy. The techniques used for merging scan tiles linearly, as well as the procedures for data processing and analysis, are detailed in the methods and results sections of this manuscript. A sperate methods section include along with data files also describe the details of the Image acquisition, preprocessing, and tiling methodology.</p>
Data file for Massé et al.'s article, "Unraveling the Life History of Past Populations through Hypercementosis: Insights into Cementum Apposition Patterns and Possible Etiologies using Micro-CT and Confocal Microscopy".
<p>This repository provides a supporting data file for the following research article:</p> <p>Massé L., d’Incau E., Souron A., Vanderesse N., Santos F., Maureille B., Le Cabec A. (2024) Unraveling the Life History of Past Populations through Hypercementosis: Insights into Cementum Apposition Patterns and Possible Etiologies Using Micro-CT and Confocal Microscopy. <em>Biology</em>, 13, 43. doi: <span><a href="https://doi.org/10.3390/biology13010043" target="_blank" rel="nofollow noopener noreferrer">10.3390/biology13010043</a></span></p> <p>For the detailed statistical analyses performed using this dataset, see Supporting Information 1 of the article.</p>
Source code and data for manuscript "Large-scale deep tissue voltage imaging with targeted illumination confocal microscopy"
<p>Source code and data for manuscript "Large-scale deep tissue voltage imaging with targeted illumination confocal microscopy", <em>Nat Methods</em> (2024), https://doi.org/10.1038/s41592-024-02275-w.</p>
Beyond the Surface: Exploring Ancient Plant Food Processing through Confocal Microscopy and 3D Surface Texture Analysis
<p>This repository contains the raw data and code to reproduce the analyses presented in the paper "Beyond the Surface: Exploring Ancient Plant Food Processing through Confocal Microscopy and 3D Surface Texture Analysis" by Zupancich et al.</p> <p>The repositiory includes:</p> <ul> <li>CSV files containing the raw data of 3D surface measurement of experimental active and passive tools utilised in processing cereals and legumes.</li> <li>Rmarkdown files of the code utilised to perform the analyses</li> </ul>
3D+time nuclei tracking dataset of confocal fluorescence microscopy time series of C. elegans embryos
<p>The dataset consists of 3 confocal microscopy time series of <em>C. elegans</em> embryos, fully tracked with StarryNite followed by manual curation</p> <ul> <li>3 raw time-series and the corresponding tracks/lineage trees</li> <li>temporal resolution; 75s</li> <li>temporal extent: 400 frames, tracked for at least 370 frames</li> <li>spatial resolution (zyx): 0.75 x 0.15 x 0.15 μm</li> <li>spatial extent (zyx):/ 41 x 512 x 512px</li> <li>Microscope: Zeiss Axio Observer.Z1</li> </ul> <p>The annotations were created using the method described in:</p> <p><em> Santella, A., Du, Z. & Bao, Z. A semi-local neighborhood-based framework for probabilistic cell lineage tracing. BMC Bioinformatics 15, 217 (2014). <a href="https://doi.org/10.1186/1471-2105-15-217">https://doi.org/10.1186/1471-2105-15-217</a></em></p> <p>Additionally the data was extended and used for the development of a new tracking method in the following publication:</p> <p><em> Hirsch, P., Malin-Mayor C., Santella, A., Preibisch, S., Kainmueller, D., Funke, J. Tracking by weakly-supervised learning and graph optimization for whole-embryo C. elegans lineages. MICCAI 2022.</em></p> <p>For questions please contact Peter Hirsch (<a href="mailto:peter.hirsch@mdc-berlin.de">peterhirsch@posteo.de</a>).</p>
Autophagosomal/autolysosomal/lysosomal dynamics of FaDu and HGFb cells affected by autophagy modulators (dataset of dual labeling of autophagosomes and labeling lysosomes, confocal microscopy)
<p>In this dataset, the impact of autophagy modulators on the auophagosomes and lysosomes in FaDu and HGF cells was investigated. Experimental details are described in the accompanying paper. This dataset contains total 702 CZI confocal image Z-stacks.</p> <p><strong>Relevant paper</strong>: HANELOVA, Klara, RAUDENSKA, Martina, KRATOCHVILOVA, Monika, NAVRATIL, Jiri, VICAR, Tomas, BUGAJOVA, Maria, GUMULEC, Jaromir, MASARIK, Michal and BALVAN, Jan. Autophagy modulators influence the content of important signalling molecules in PS-positive extracellular vesicles. <em>Cell Communication and Signaling</em>. 24 May 2023. Vol. 21, no. 1, p. 120. DOI <a href="https://doi.org/10.1186/s12964-023-01126-z">10.1186/s12964-023-01126-z</a>.</p> <div> <div> <div> </div> </div> </div> <p><strong>Model cell lines</strong></p> <p> </p> <p>The cell line FaDu (HTB-43TM), derived from a squamous cell carcinoma (SCC) of the hypopharynx, and the human gingival fibroblast cell line HGF (derived from the histologically normal gingival biopsy) were used in this study. The authenticated cell lines were purchased from the American Type Culture Collection (ATCC; Manassas, Virginia, USA) within the last five years. </p> <p><strong>Autophagy modulation</strong></p> <p>For autophagy modulation, FaDu cells were treated for 24 h with 5nM bafilomycin A1 (Sigma-Aldrich, B1793), 50 µM of hydroxychloroquine sulphate (Sigma-Aldrich, H0915), 100 µM of Cpd18 (Calbiochem), 50 nM of autophinib (Sigma, SML2632), 10 µM of EACC (MedChemExpress), 200 nM of rapamycin (Sigma-Aldrich, R0395), 3 nM of Torin-1 (MedChemExpress), or 30 nM of NVP-BEZ235 (MedChemExpress). To induce starvation, cells were cultured in DMEM F12 without glutamine and without FBS (Biosera). Modulation of autophagy did not reduce the viability of FaDu cells.</p> <p><strong>Conditioned media preparation</strong></p> <p>see details in the accompanying paper</p> <p><strong>Fluorescence Microscopy</strong><br>The autophagosomal/autolysosomal/lysosomal dynamics of affected cells were observed using the combination of PremoTM Autophagy Tandem Sensor (P36239, Invitrogen) with the far-red emitting LysoTracker® Deep Red (L12492, Invitrogen) (Ex 647 nm/Em 668 nm). By combining acid-sensitive Emerald GFP (Ex 488 nm/Em 509 nm) with acid-insensitive TagRFP (Ex 555 nm/Em 584 nm) in the PremoTM kit, autophagosomes and autolysosomes labelling (yellow and red, respectively) is possible.<br>Immediately after transduction with 12 µl PremoTM Autophagy Tandem Sensor/2ml cell suspension, cells were seeded at 5 × 10<sup>5</sup> into 35-mm glass-bottomed gelatin-coated dishes (Ibidi, μ-Dish 35 mm, high Glass Bottom) and cultured for 48 h to equilibrate expression levels. Subsequently, cells were exposed to the selected agents for 6, 12, 24 and 48 hours before imaging. LysoTracker® Deep Red staining was performed 1 h before imaging. <br>To monitor the uptake of isolated PS-EVs by fibroblasts, we stained EVs with PKH67 (Sigma, PKH67GL) and then removed the remaining dye using Exosome Spin Columns (MW 3000) (Thermo Scientific, #4484449). The stained EVs were then suspended in 400 ul of cultivation medium and added to HGFB cells growing for 24 h in Ibidi µ-Slide I Luer (Ibidi, 80176). Image acquisition was performed 24 hours after EVs addition. 1 µl of 1 µg/ml of Hoechst 33342 (Enzo) (Ex 350 nm/ Em 461 nm) nuclear stain was added 1 hour before imaging.<br>To determine the viability of the cell population prior to isolation of EVs, cells were left in a culture dish with 1 ml of culture medium to which propidium iodide (Sigma-Aldrich) and Hoechst 33342 were added 45 minutes before capturing. <br>To maximize the possibility of comparison between samples, all samples (from a single cell line) were captured on the same day in a single run using the same microscope settings. For each time and each treatment, 10–12 fields of view were captured from randomized sites of the culture dish. Epifluorescent microscopy images and confocal microscopy images were acquired using Laser scanning confocal microscope Zeiss LSM 880 with AiryscanFast module (Carl Zeiss Inc.) using a C-apochromat 40x/1.20 W and C-Apochromat 63 /1.20 W. LysoTracker® Deep Red was excited HeNe 633 nm solid-state laser and emitted light was detected at 638–759 nm. Emerald GFP was excited 488 nm ArgonRemote laser, and emitted light was detected at 493–576 nm. TagRFP was excited DPSS 561 nm laser, and emitted light was detected at 570–650 nm. Hoechst 33342 was excited with a 405 nm solid-state laser, and emitted light was detected at 410–508 nm. Fluorescence images were acquired by the transmitted light detector. <br>Images were analyzed using ImageJ software and custom MATLAB software developed in our laboratory. The analysis process consists of the segmentation of cells from the background and extraction of the intensity of fluorescence channels (TagRFP, GFP, LysoTracker) inside cells. For segmentation, a thresholding-based method was used, where a manually selected threshold was applied. Segmentation was applied to the image created as the sum of all fluorescence channels to achieve segmentation independent of the intensity of individual channels. To achieve better segmentation without noisy pixels, fluorescence images were preprocessed with median filter (7x7) and Gaussian filter (standard deviation 1); additionally, binary segmentation was post-processed with morphological closing and removal of small binary connected components (<5000px). For intensity extraction, the mean value of segmented cell pixels was used for each field of view. Besides individual fluorescence channels, the mean colocalization of TagRFP and GFP was calculated with a pixel-wise multiplication of TagRFP and GFP channels.</p> <p><strong>File Naming</strong></p> <p>CZI images are organised in folders according to cell line, treatment time, and treatment. Names include magnification, cell line measured, treatment, and time of treatment,</p> <blockquote> <p>40x_FADU_BAF_12h_BF_4.czi</p> </blockquote> <p>The abbreviations used for treatments are as follows: BAF, bafilomycin A1; HCQ, hydroxychloroquine sulphate; Cpd18; APB, autophinib; EACC; RAPA, rapamycin; TOR1, Torin-1; BEZ, NVP-BEZ235; starv, starvation; </p>
Annotated and processed 3D confocal microscopy images of dorsal aorta in wild-type and Endoglin-deficient zebrafish embryos at 48 hpf and 72 hpf
<p>This repository contains the original 3D confocal microscopy images that were used for the analysis of vessel geometry and endothelial cell morphology in the dorsal aorta of wild-type and Endoglin-deficient zebrafish embryos at 48 hours post fertilization (hpf) and 72 hpf in the article <a href="https://www.biorxiv.org/content/10.1101/2024.02.19.580931">Novel mathematical approach to accurately quantify 3D endothelial cell morphology and vessel geometry based on fluorescently marked endothelial cell contours: Application to the dorsal aorta of wild-type and Endoglin-deficient zebrafish embryos</a>. In this article, we developed a novel mathematical approach that allows to consistently estimate 3D vessel geometry and endothelial cell surface morphology using only information from endothelial cell contours. For the article's analysis, endothelial cell contours were manually annotated on Pecam1-EGFP-labeled cell junctions. Furthermore, dorsal aorta cross-sections were outlined on Dextran Texas Red-perfused vessel lumens. Further details are provided in the article's Materials and methods section.</p> <p>This repository contains 14 images of 7 wild-type embryos, each imaged at 48hpf and 72hpf. Furthermore, 12 images of 6 Endoglin-deficient embryos, each imaged at 48hpf and 72hpf are included. These combined files (called "analysis data" in the article) are stored in "eng_wt_data.zip". Secondly, images of 2 wild-types at 72hpf with repeated cell contour annotation and outlined vessel lumens (called "validation data" in the article) are located in "wt_angiogram_data.zip". The provided files are stored in Imaris format and can be inspected using the free <a href="https://imaris.oxinst.com/imaris-viewer">Imaris Viewer software</a>.</p> <p>To allow inspection of the endothelial cell contours that we manually annotated for the article's analysis and compare them against the intermediate results of our novel mathematical approach, i.e., contour enrichments by neighboring cells, contour smoothing splines and their projections onto the estimated vessel surfaces, we imported these contours into the Imaris files. Note that the contours' coordinates in these files are slightly less precise than in our article's analysis and thus are intended for visual inspection. To exactly reproduce the results in our article, refer to the files in <a href="https://doi.org/10.5281/zenodo.10549101">our other Zenodo repository</a>.</p>
Confocal microscopy of gH2AX and 53BP1 DNA repair foci of cells exposed to gamma-irradiation, pt. 2/3
<p><strong>Summary</strong></p> <p>Dataset of confocal microscopy data of cells exposed to gamma-irradiation and immunostained with gH2AX and 53BP1.</p> <ul> <li><strong>Part 1/3: </strong>Head and neck primocultures immunostained with gH2AX/53BP1, Testing dataset. DOI <a href="https://doi.org/10.5281/zenodo.2564980">10.5281/zenodo.2564980</a></li> <li><strong>Part 2/3 (this dataset)</strong>: U-87 and NHDF Cells exposed to 1-4 Gy confocal microscopy data of head and neck tumor primocultures immunostained with gH2AX/53BP1. Testing dataset. DOI <a href="https://doi.org/10.5281/zenodo.2572450">10.5281/zenodo.2572450</a>. 174 TIFFs</li> <li><strong>Part 3/3</strong>: training dataset for nuclei and gH2AX foci with ground truth annotation masks, head and neck primocultures (head and neck non-tumor and spinocellular tumor cells). DOI <a href="https://doi.org/10.5281/zenodo.2576241">10.5281/zenodo.2576241</a>. 150 TIFFs for nuclei learning incl 150 png nuclei masks + 99 TIFFs for DNA repair foci training</li> <li><strong>Code</strong>: the code is available at <a href="https://github.com/tomasvicar/LearnFoci">https://github.com/tomasvicar/LearnFoci</a></li> </ul> <p><strong>Materials and methods</strong></p> <p><em>Dataset</em></p> <p>Following cells were used: (1) patient primocultures of patients with spinocellular head and neck tumors (histologically verified tumor and tumor-adjacent tissues), isolation protocol descibed in <em>Svobodova et al, 2017</em>, (2) primary glioblastoma cell line U-87 (ATCC HTB-14, LGC Standards, United Kingdom), (3) primary normal human dermal fibroblasts (NHDF, PromoCell, Hedelberg, Germany) isolated from the dermis of juvenile foreskin or adult skin.<br> The study was conducted in accord with the Helsinki Declaration of 1964 and all subsequent revisions thereof. It was approved by the ethical committee of St. Anne’s Faculty Hospital, Brno. Primoculture cells were cultivated in Pen/Strep antibiotic solution (PAA Laboratories GmbH, Austria) in RPMI-1640 medium with 10% FBS (Biochrom, USA) at 37 °C and 50% CO2 in humidified atmosphere up to 50% confluence. U-87 were grown in Eagle's MEM with 10% FBS.</p> <p><em>Gamma irradiation</em></p> <p>The cells were irradiated at the Institute of Biophysics, Czech Academy of Sciences, Brno, Czech Republic in a following schemes: (a) patient-derived primoculture was irradiated with a single dose of 2 Gy (D = 1 Gy/min) of gamma-rays (60Co, Chisostat, Chirana, CR) , (b) U-87 and NHDF cells were irradiated with doses 1, 2, and 4 Gy (D = 1 Gy/min). Cells were irradiated in RPMI 1640 medium (37 °C, normal atmosphere). Confocal microscopy of gammaH2AX and 53BP1 foci immunodetection was consequently performed.</p> <p><em>Fluorescent staining </em></p> <p>DNA double strand breaks (DSBs) were quantified in different periods of time post-irradiation (30 min, 8h and 24h post irradiation) by means of $\gamma$H2AX and 53BP1 foci immunodetection combined with confocal microscopy. For details see \cite{falk2007chromatin}.</p> <p><em>Confocal microscopy</em></p> <p>The microscopy of samples was performed at the Institute of Biophysics, Czech Academy of Sciences, Brno, Czech Republic. Leica DM RXA microscope (equipped with DMSTC motorized stage, Piezzo z-movement, MicroMax CCD camera, CSU-10 confocal unit and 488, 562, and 714 nm laser diodes with AOTF) was used for acquiring detailed cell images (100× oil immersion Plan Fluotar lens, NA 1.3). Total 50 Z slices was captured with Z step size 0.3 μm.</p> <p><strong>File description</strong></p> <p>all files are compressed hyperstack tiffs (50 Z slices and 3 fluorescent channels, XYCZ order), 100x magnification</p> <ul> <li>Confocal_NHDF_cells_IR_1-4Gy.zip: Human fibroblast NHDF cell line, exposed to gamma irradiation doses 1, 2, and 4 Gy, 64 TIFFs</li> <li>Confocal_U-87_cells_IR_1-4Gy.zip: Human glioblastoma U-87 cell line, exposed to gamma irradiation doses 1, 2, and 4 Gy, 108 TIFFs</li> </ul>
Confocal microscopy of gH2AX and 53BP1 DNA repair foci of cells exposed to gamma-irradiation, pt. 1/3
<p><strong>Summary</strong></p> <p>Dataset of confocal microscopy data of cells exposed to gamma-irradiation and immunostained with gH2AX and 53BP1.</p> <ul> <li><strong>Part 1/3 (this dataset): </strong>Head and neck primocultures immunostained with gH2AX/53BP1, Testing dataset. DOI <a href="https://doi.org/10.5281/zenodo.2564980">10.5281/zenodo.2564980</a></li> <li><strong>Part 2/3</strong>: U-87 and NHDF Cells exposed to 1-4 Gy confocal microscopy data of head and neck tumor primocultures immunostained with gH2AX/53BP1. Testing dataset. DOI <a href="https://doi.org/10.5281/zenodo.2572450">10.5281/zenodo.2572450</a>. 174 TIFFs</li> <li><strong>Part 3/3</strong>: training dataset for nuclei and gH2AX foci with ground truth annotation masks, head and neck primocultures (head and neck non-tumor and spinocellular tumor cells). DOI <a href="https://doi.org/10.5281/zenodo.2576241">10.5281/zenodo.2576241</a>. 150 TIFFs for nuclei learning incl 150 png nuclei masks + 99 TIFFs for DNA repair foci training</li> <li><strong>Code</strong>: the code is available at <a href="https://github.com/tomasvicar/LearnFoci">https://github.com/tomasvicar/LearnFoci</a></li> </ul> <p><strong>Materials and methods</strong></p> <p><em>Dataset</em></p> <p>Following cells were used: (1) patient primocultures of patients with spinocellular head and neck tumors (histologically verified tumor and tumor-adjacent tissues), isolation protocol descibed in <em>Svobodova et al, 2017</em>, (2) primary glioblastoma cell line U-87 (ATCC HTB-14, LGC Standards, United Kingdom), (3) primary normal human dermal fibroblasts (NHDF, PromoCell, Hedelberg, Germany) isolated from the dermis of juvenile foreskin or adult skin.<br> The study was conducted in accord with the Helsinki Declaration of 1964 and all subsequent revisions thereof. It was approved by the ethical committee of St. Anne’s Faculty Hospital, Brno. Primoculture cells were cultivated in Pen/Strep antibiotic solution (PAA Laboratories GmbH, Austria) in RPMI-1640 medium with 10% FBS (Biochrom, USA) at 37 °C and 50% CO2 in humidified atmosphere up to 50% confluence. U-87 were grown in Eagle's MEM with 10% FBS.</p> <p><em>Gamma irradiation</em></p> <p>The cells were irradiated at the Institute of Biophysics, Czech Academy of Sciences, Brno, Czech Republic in a following schemes: (a) patient-derived primoculture was irradiated with a single dose of 2 Gy (D = 1 Gy/min) of gamma-rays (60Co, Chisostat, Chirana, CR) , (b) U-87 and NHDF cells were irradiated with doses 1, 2, and 4 Gy (D = 1 Gy/min). Cells were irradiated in RPMI 1640 medium (37 °C, normal atmosphere). Confocal microscopy of gammaH2AX and 53BP1 foci immunodetection was consequently performed.</p> <p><em>Fluorescent staining </em></p> <p>DNA double strand breaks (DSBs) were quantified in different periods of time post-irradiation (30 min, 8h and 24h post irradiation) by means of $\gamma$H2AX and 53BP1 foci immunodetection combined with confocal microscopy. For details see \cite{falk2007chromatin}.</p> <p><em>Confocal microscopy</em></p> <p>The microscopy of samples was performed at the Institute of Biophysics, Czech Academy of Sciences, Brno, Czech Republic. Leica DM RXA microscope (equipped with DMSTC motorized stage, Piezzo z-movement, MicroMax CCD camera, CSU-10 confocal unit and 488, 562, and 714 nm laser diodes with AOTF) was used for acquiring detailed cell images (100× oil immersion Plan Fluotar lens, NA 1.3). Total 50 Z slices was captured with Z step size 0.3 μm.</p> <p><strong>File description</strong></p> <p>all files are compressed hyperstack tiffs (50 Z slices and 3 fluorescent channels, XYCZ order), 100x magnification</p> <ul> <li>Confocal_HN_tumor_primocultures.zip: dataset of patient-derived primocultures (gamma-irradiated with 2 Gy and controls), for description see file below, 100 FOVs,</li> <li>Confocal_HN_tumor_primocultures_description.xlsx: description of confocal dataset files and patient tumor characteristics</li> <li>Confocal_HN_tumor_primocultures_train_nuclei.zip: annotated training subset 1 of dataset of patient-derived primocultures (gamma-irradiated with 2 Gy and controls) used for nuclei segmentation training, 150 FOVs, includes TIFF and manually annotated binary mask for nuclei (data_###.tif and respective mask_###.png)</li> <li>Confocal_HN_tumor_primocultures_train_nuclei_description.xlsx: description of above-mentioned files (tissue type, TNM stage, grade, time post irradiation)</li> </ul>
Annotated DNA Double Strand Break Ionizing Radiation-Induced Foci (gH2AX 53BP1) Confocal Microscopy, pt. 2
<p><strong>Summary</strong></p> <p>Dataset of confocal microscopy data of cells exposed to gamma-irradiation and immunostained with gH2AX and 53BP1.</p> <ul> <li>Nuclei segmentation Head and neck primocultures immunostained with gH2AX/53BP1, Training/Testing/Validation dataset (nucleus_segmentation.zip) (available in part 1, <a href="https://dx.doi.org/10.5281/zenodo.4067741">https://dx.doi.org/10.5281/zenodo.4067741</a>) </li> <li>IRIF Foci: Head and neck primocultures immunostained with gH2AX/53BP1, Training/Testing/Validation dataset. (foci_detection.zip) (available in part 1, <a href="https://dx.doi.org/10.5281/zenodo.4067741">https://dx.doi.org/10.5281/zenodo.4067741</a>)</li> <li>Cell lines: U-87 and NHDF Cells exposed to 0.5-8 Gy 30 min and 8h post irradiation - confocal microscopy data of gH2AX/53BP1/DAPI annotated for gH2AX, 53BP1 and colocalized foci separately (cell_lines_U87.zip and cell_lines_NHDF.zip, this part of dataset) </li> <li><strong>Code</strong>: the code is available at <a href="https://github.com/tomasvicar/DeepFoci">https://github.com/tomasvicar/DeepFoci</a></li> <li><strong>Preprint: </strong>Vicar et al, DeepFoci: Deep Learning-Based Algorithm for Fast Automatic Analysis of DNA Double Strand Break Ionizing Radiation-Induced Foci, <a href="https://doi.org/10.1101/2020.10.07.321927">10.1101/2020.10.07.321927</a></li> <li><strong>Publication: </strong>Vicar et al, TBA</li> </ul> <p><strong>Materials and methods</strong></p> <p><em>Dataset</em></p> <p>Following cells were used:</p> <p>1) The training/validation/testing datasets was based on patient-derived primary cell cultures prepared from spinocellular tumors and morphologically normal tissues adjacent to the tumor taken from patients suffering from head and neck cancer. The dataset was divided into two subsets: one for training, validation and testing the nucleus segmentation (237/10/30 fields of view (FOVs), respectively) and one for training, validation and testing the focus segmentation (239/60/100 FOVs). The dataset consisted of several cell types: a) tumor cells, b) tumor-associated fibroblasts, and c) cells from morphologically normal tissues. All cell types were fixed at different periods of time (0 (non-irradiated control), 0.5, 8 or 24 h PI) after exposure to 2 Gy of gamma-rays. The representation of cells in two subsets with respect to the cell type and post-irradiation time (i.e., DSB repair duration) was random.</p> <p>2) The evaluation dataset was used to assess the robustness of segmentation procedures. It was composed of multiple types of differently treated cells in order to represent a highly challenging dataset maximally reflecting high biological and technical variability between samples, as it may appear in research or clinical practice. The dataset contained a) mesenchymal NHDF fibroblasts coming from a standard permanent cell line, b) radioresistant U-87 glioblastoma cells coming from a standard permanent cell line, c) tumor cells (CD90-) and tumor-associated fibroblasts (CD90+) prepared as a primary culture from a spinocellular tumors of patients (different from dataset 1) suffering from a head and neck cancer, and d) cells prepared as primary cultures from morphologically normal tissue adjacent to tumors of involved head and neck cancer patients. NHDF and U-87 cells received 0.5, 0, 1, 2, 4 and 8 Gy of gamma-rays and were fixed at 30 min and 8 h post-irradiation, while the primary cultures were only exposed to the dose of 2 Gy (for a limited amount of the cell material) and fixed at 0 (non-irradiated control), 0.5, 8 or 24 h post-irradiation times.</p> <p><em>Gamma irradiation</em></p> <p>The cells were irradiated at the Institute of Biophysics, Czech Academy of Sciences, Brno, Czech Republic in a following schemes: (a) patient-derived primoculture was irradiated with a single dose of 2 Gy (D = 1 Gy/min) of gamma-rays (60Co, Chisostat, Chirana, CR) , (b) U-87 and NHDF cells were irradiated with doses 0.5-8 Gy (D = 1 Gy/min). Cells were irradiated in RPMI 1640 medium (37 °C, normal atmosphere). Confocal microscopy of gammaH2AX and 53BP1 foci immunodetection was consequently performed.</p> <p><em>Fluorescent staining</em></p> <p>DNA double strand breaks (DSBs) were quantified in different periods of time post-irradiation (30 min, 8h and 24h post irradiation) by means of $\gamma$H2AX and 53BP1 foci immunodetection combined with confocal microscopy. For details see \cite{falk2007chromatin}.</p> <p><em>Confocal microscopy</em></p> <p>The microscopy of samples was performed at the Institute of Biophysics, Czech Academy of Sciences, Brno, Czech Republic. Leica DM RXA microscope (equipped with DMSTC motorized stage, Piezzo z-movement, MicroMax CCD camera, CSU-10 confocal unit and 488, 562, and 714 nm laser diodes with AOTF) was used for acquiring detailed cell images (100× oil immersion Plan Fluotar lens, NA 1.3). Total 50 Z slices was captured with Z step size 0.3 μm.</p> <p><strong>File description</strong></p> <p>all files are compressed hyperstack tiffs (50 Z slices and 3 fluorescent channels, XYCZ order), 100x magnification</p> <ul> <li>foci_detection.zip: IRIF Foci (available in part 1, <a href="https://dx.doi.org/10.5281/zenodo.4067741">https://dx.doi.org/10.5281/zenodo.4067741</a>): Head and neck primocultures immunostained with gH2AX/53BP1, Training/Testing/Validation dataset: FOVs 240/100/120 files for training, testing, and validation, organisation: <ul> <li>data_001.tif – 3channel Z.stack tiff</li> <li>mask_001.tif – respective Z stack mask with single points per IRIF focus (manual annotation, training and testing subsets only)</li> <li>data_description.xlsx – description of sample type (2Gy post irradiation times and characteristics of primary culture of squamous cell cancer of patients)</li> <li>data_001_pos.csv – manual annotation of gH2AX/53BPI IRIF foci by two experts – cordinates file (in 2D, validation only)</li> </ul> </li> <li>nucleus_segmentation.zip (available in part 1, <a href="https://dx.doi.org/10.5281/zenodo.4067741">https://dx.doi.org/10.5281/zenodo.4067741</a>) Nuclei segmentation Head and neck primocultures immunostained with gH2AX/53BP1, FOVs 237 Training/ 30 Testing/ 10 Validation dataset <ul> <li>data_001.tif – 3channel Z.stack tiff</li> <li>mask_001.tif – respective Z stack mask with manually annotated nucleus mask (manual annotation, training and testing subsets only)</li> <li>data_description.xlsx – description of sample type (2Gy post irradiation times and characteristics of primary culture of squamous cell cancer of patients)</li> </ul> </li> <li>U87.zip and NHDF.zip: Annotated gH2AX/53BP1 foci in cell lines exposed to increasing dose, annotations performed for gH2AX, 53BP1 and colocalized focus separatelly. 679 annotated FOVs for both cell lines. <ul> <li>control.png - RGB control figure showing merge and annotated overlay</li> <li>data_53BP1.tif - TIFF Z-stack, confocal microcopy, 53BP1 channel</li> <li>data_DAPI.tif - TIFF Z-stack, confocal microcopy, DAPI channel</li> <li>data_gH2AX.tif - TIFF Z-stack, confocal microcopy, gH2AX channel</li> <li>labels.json - foci labels for individual channel</li> <li>mask.tif - generated Z-stack of nucleus mask</li> </ul> </li> </ul>
Confocal microscopy imaging of FocalCheck fluorescent beads at various oil indices under ambient temperature
<p>the dataset consisting of 20 fields of images with physical dimensions of 1340x1340x64 pixels. These images were acquired using two different refractive indices: one with oil immersion corrected for a temperature of 23°C and another with oil immersion corrected for a temperature of 37°C. A constant temperature of 24.5°C was maintained throughout the data collection</p>
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.