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.
473
datasets available to search
ShareScore release 0.9.0
Dataset results
473 results for “confocal”
Fig. 2 Tomopteris pacifica. Neurogenesis. Confocal maximum projections. A in Development and structure of the anterior nervous system and sense organs in the holopelagic annelid Tomopteris spp. (Phyllodocida, Errantia)
Fig. 2 Tomopteris pacifica. Neurogenesis. Confocal maximum projections. A Early developmental stages are characterized by a large amount of yolk and a prominent prototroch (pt). B At 5 days post-fertilization (dpf), the larval stages possess four pairs of well-developed trunk appendages and a distinct prototroch (pt). Note that the anterior-most appendage (I) is uniramous while all other appendages appear biramous. C Slightly older stages show a well-developed ventral nerve cord (vnc) with outgoing parapodial neurite bundles (pn) innervating the body appendages; serotonergic somata form serial clusters along the ventral nerve cord. D A closer examination of larvae at around 6–7 dpf shows the presence of a prominent nuchal nerve (nn) innervating the nuchal organs and originating from the dorsal part of the larval brain (br). The insert shows the innervation of the nuchal organ.
Sparks et al, Heterogeneity in tumor chromatin-doxorubicin binding revealed by in vivo fluorescence lifetime imaging confocal endomicroscopy: In vitro data
<p>Data is divided into three folders:</p> <ul> <li>Sparks_et_al_FIG2_Histone_vs_free_GFP <ul> <li>data for Sparks et al Figure 2</li> <li>main text section: <em>'FRET between chromatin-bound GFP and doxorubicin'</em></li> </ul> </li> <li>Sparks_et_al_FIG3_in_vitro_dose_response <ul> <li>data for Sparks et al Figure 3#</li> <li>main text section:<em> 'FLIM endomicroscope can monitor doxorubicin cellular uptake'</em></li> </ul> </li> <li>Sparks_et_al_SuppFIG2_endoscope_spectral_cross_talk <ul> <li>data for Sparks et al Supplementary Figure 2</li> <li>Supplementary information</li> </ul> </li> </ul> <p><strong>Cell lines</strong></p> <p>IGROV-1 cell lines were cultured in CO<sub>2</sub> dependent media with 10% fetal bovine serum and 1% Pen Strep at 37 ˚C. Before experiments, cells were grown to 80% confluence. For measuring doxorubicin uptake by fluorescence an IGROV-1 cell line stably expressing GFP fused to Histone-1 (H1) was made using the PiggyBac transposon system. As a control to show that effect of doxorubicin on GFP depends on whether it is fused to H1 or not, a stable whole cell expression of GFP by lentiviral transfection and selection by Geneticin was made. For bioluminescence imaging of xenograft tumors, all IGROV-1 cell lines were made to stably express firefly luciferase.</p> <p>To investigate the effect of doxorubicin on other histones, IGROV-1 cells were transiently transfected with a Histone-2B-GFP plasmid (gift from Kurt Anderson) using the Lipofectamine® 2000 reagent.</p> <p>IGROV-1 cells were obtained from Crick institute cell services and confirmed as IGROV-1 by Short Tandem Repeats (STR) profiling and no mycoplasma was detected.</p> <p><strong>In vitro experiments</strong></p> <p>IGROV-1 cells were grown to 80% confluence in 75 ml flasks before being re-plated in 12 or 24 well plates or 35 ml glass bottomed dishes and allowed to attach to the surface for 24 hours before experiments.</p> <p>To study how the fluorescence of GFP labelled H1 labelled IGROV-1 cells changes with doxorubicin treatment, fluorescence intensity and lifetime distributions were measured from cells after 3 hours of incubation with doxorubicin of varying concentrations (0, 0.18, 0.9, 1.8, 9, 18 µM) by serial dilutions of a stock solution with PBS. After 3 of hours, cells were washed in PBS then fixed for 20 minutes in 4% PFA. Cells were then imaged in PBS. Doxorubicin hydrochloride (Sigma-Aldrich, D1515-10 mg) was dissolved in PBS to a concentration of 9 mM and stored at -20˚C.</p>
Sparks et al, Heterogeneity in tumor chromatin-doxorubicin binding revealed by in vivo fluorescence lifetime imaging confocal endomicroscopy: in vivo data
<p>Data is divided into three folders:</p> <ul> <li>Sparks_et_al_FIG_6_IP_intranodule_heterogeneity <ul> <li>data for Sparks et al Figure 6</li> <li>main text section: <em>'FRET between chromatin-bound GFP and doxorubicin'</em></li> </ul> </li> <li>Sparks_et_al_FIG4_5_6_IP_IV_chemo_comparison <ul> <li>data for Sparks et al Figures 4,5 & 6</li> <li>main text section:<em> 'FLIM endomicroscope can monitor doxorubicin cellular uptake'</em></li> </ul> </li> <li>Sparks_et_al_FIG6_IP__internodule_heterogeneity <ul> <li>data for Sparks et al Figure 6</li> <li>main text section: <em>'Intra-tumor heterogeneity'</em></li> </ul> </li> </ul> <p><strong>In vivo experiments</strong></p> <p>Murine xenografts were prepared by intraperitoneal (IP) injection of IGROV-1 cancer cells. IGROV-1 cells were grown to 80% confluence before being trypsinized and re‑suspended in PBS at a concentration of cells per ml. cells were injected into ICRF nude mice. After 14 days post-injection, the presence of intraperitoneal tumors was confirmed by bioluminescence imaging. Briefly, an IVIS bioluminescence imaging system was used to image isoflurane anesthetized mice. 100 µl of D-luciferin (luciferase substrate) at 30mg ml<sup>-1</sup> was injected IP 10 minutes before recording of bioluminescence images. The presence of peritoneal tumors was confirmed if bioluminescence signals from the peritoneum were above background noise 10-30 minutes after D‑luciferin injections. Following confirmation of tumors, in vivo fluorescence imaging experiments were carried out after 21 days. To study differences in drug uptake between intravenous or intraperitoneal delivery, prior to imaging mice were subject to IP or IV doxorubicin-based chemotherapy for 1.5, 3 or 24 hours. Imaging involved terminal procedures, mice were anesthetized then peritoneal tumors were exposed by minor surgery and inspected with the CEM.</p> <p>All animal model procedures were approved by The Francis Crick Institute Biological Ethics Committee and UK Home Office authority provided by Project License 70/8380.</p> <p> </p> <p> </p>
Dataset of confocal microscopy stacks from plant samples - ImageJ SurfCut: a user-friendly, high-throughput pipeline for extracting cell contours from 3D confocal stacks
<p>This data set contains confocal stacks from <em>Arabidopsis thaliana </em><em>35S::GFP-MBD</em> light grown hypocotyl as well as propidium iodide stained cotyledon pavement cells and shoot apical meristem. This is the test dataset for the Fiji macro SurfCut (https://github.com/sverger/SurfCut; 10.5281/zenodo.2635737)</p> <p> </p> <p><strong>Material and methods:</strong></p> <p>Plant material and growth conditions</p> <p><em>Arabidopsis thaliana </em>wild type Col-0 and the microtubule reporter line <em>GFP-MBD</em> (WS-4, (Marc et al. 1998) were used. Seeds were cold treated for 48 hr to synchronize germination. Plants were then grown in a phytotron at 20°C, in a 16 hr light/8 hr dark cycle on solid Murashige and Skoog medium (MS medium, Duchefa, Haarlem, the Netherlands) with 0.8% agar, 1% sucrose, and no vitamin.</p> <p> </p> <p>Confocal microscopy</p> <p>Cell contour staining in the case of PC_PI_Col0_(1-8).tif and SAM_PI_Col-0.tif was performed by staining the cell wall with Propidium Iodide (PI). Plants were immersed in 0.2 mg/ml propidium iodide (PI, Sigma-Aldrich) for 10 min and washed with water prior to imaging. For imaging, samples were either placed on a solid agar medium and immersed in water, or placed between glass slide and coverslip separated by 400 μm spacers to prevent tissue crushing. Images were acquired using a Leica TCS SP8 confocal microscope, equipped with a water immersion objective (HCX IRAPO L 25x/0.95 W). PI excitation was performed using a 552 nm solid-state laser and fluorescence was detected at 600–650 nm. GFP excitation was performed using a 488 nm solid-state laser and fluorescence was detected at 495–535 nm. Stacks of 1024x1024 pixels (pixel size of 0.363 x 0.363 micron) optical section were generated with a Z interval of 0.5 μm.</p> <p> </p> <p><strong>File list:</strong></p> <p>Light grown hypocotyl, <em>GFP-MBD</em> reporter line:</p> <p>- Hypocotyl_GFP-MBD.tif</p> <p>Cotyledon’s pavement cells, PI staining:</p> <p>- PC_PI_Col0_1.tif</p> <p>- PC_PI_Col0_2.tif</p> <p>- PC_PI_Col0_3.tif</p> <p>- PC_PI_Col0_4.tif</p> <p>- PC_PI_Col0_5.tif</p> <p>- PC_PI_Col0_6.tif</p> <p>- PC_PI_Col0_7.tif</p> <p>- PC_PI_Col0_8.tif</p> <p>Shoot apical meristem, PI staining:</p> <p>- SAM_PI_Col-0.tif</p> <p> </p> <p><strong>Reference:</strong></p> <p>Marc, Jan, Cheryl L. Granger, Jennifer Brincat, Deborah D. Fisher, Teh-hui Kao, Andrew G. McCubbin, and Richard J. Cyr. 1998. “A GFP–MAP4 Reporter Gene for Visualizing Cortical Microtubule Rearrangements in Living Epidermal Cells.” <em>The Plant Cell</em> 10 (11): 1927–39. https://doi.org/10.1105/tpc.10.11.1927.</p>
Systematic assessment of burst impurity in confocal-based single-molecule fluorescence detection using Brownian motion simulations - photon timetag simulation files
<p>Attached are the photon timestamp and channels simulated for different 3D diffusing molecules simulations at different conditions (simulation was performed by PyBroMo).</p> <p>Each of the files has, in its name, a code. The meaning of the codes are as following:</p> <pre>f32445 - 15 molecules at a concentration of 62 pM, with a diffusion coefficient of 90 micron^2/s - 60 second simulation using a numerical PSF model </pre> <pre>a01f8f - 15 molecules at a concentration of 31 pM, with a diffusion coefficient of 90 micron^2/s - 60 second simulation using a numerical PSF model</pre> <pre>9ff667 - 15 molecules at a concentration of 15.5 pM, with a diffusion coefficient of 90 micron^2/s - 60 second simulation using a numerical PSF model</pre> <pre>71154a - 15 molecules at a concentration of 62 pM, with a diffusion coefficient of 22.5 micron^2/s - 60 second simulation using a numerical PSF model</pre> <pre>ad926d - 15 molecules at a concentration of 62 pM, with a diffusion coefficient of 5.625 micron^2/s - 60 second simulation using a numerical PSF model</pre> <pre>1ab235 - 15 molecules at a concentration of 62 pM, with a diffusion coefficient of 90 micron^2/s - 180 second simulation using a numerical PSF model</pre> <pre>d00978 - 15 molecules at a concentration of 62 pM, with a diffusion coefficient of 5.625 micron^2/s - 180 second simulation using a numerical PSF model</pre> <p> </p> <pre>2469bb - 15 molecules at a concentration of 62 pM, with a diffusion coefficient of 90 micron^2/s - 60 second simulation using a Gaussian PSF model </pre> <pre>4be121 - 15 molecules at a concentration of 31 pM, with a diffusion coefficient of 90 micron^2/s - 60 second simulation using a Gaussian PSF model</pre> <pre>a7088f - 15 molecules at a concentration of 15.5 pM, with a diffusion coefficient of 90 micron^2/s - 60 second simulation using a Gaussian PSF model</pre> <pre>023983 - 15 molecules at a concentration of 62 pM, with a diffusion coefficient of 22.5 micron^2/s - 60 second simulation using a Gaussian PSF model</pre> <pre>653f61 - 15 molecules at a concentration of 62 pM, with a diffusion coefficient of 5.625 micron^2/s - 60 second simulation using a Gaussian PSF model</pre> <pre>4f06ee - 15 molecules at a concentration of 62 pM, with a diffusion coefficient of 90 micron^2/s - 180 second simulation using a Gaussian PSF model</pre> <pre>dec32c - 15 molecules at a concentration of 62 pM, with a diffusion coefficient of 5.625 micron^2/s - 180 second simulation using a Gaussian PSF model</pre> <p> </p> <pre>85b0a1 - 15 molecules at a concentration of 62 pM, with a diffusion coefficient of 90 micron^2/s , 10 of which belong to a sub-population with a mean FRET efficiency of 0.75, and the leftover 5 belong to another sub-populations with a mean FRET efficiency of 0.50 - 60 second simulation using a Numerical PSF model</pre> <pre>964ef3 - 15 molecules at a concentration of 62 pM, with a diffusion coefficient of 90 micron^2/s , 10 of which belong to a sub-population with a mean FRET efficiency of 0.75, and the leftover 5 belong to another sub-populations with a mean FRET efficiency of 0.50 - 180 second simulation using a Numerical PSF model</pre> <p> </p> <pre>f28f6e - 15 molecules at a concentration of 62 pM, with a diffusion coefficient of 90 micron^2/s , 10 of which belong to a sub-population with a mean FRET efficiency of 0.75, and the leftover 5 belong to another sub-populations with a mean FRET efficiency of 0.50 - 60 second simulation using a Gaussian PSF model</pre> <pre>c311dd - 15 molecules at a concentration of 62 pM, with a diffusion coefficient of 90 micron^2/s , 10 of which belong to a sub-population with a mean FRET efficiency of 0.75, and the leftover 5 belong to another sub-populations with a mean FRET efficiency of 0.50 - 180 second simulation using a Gaussian PSF model</pre>
FIGURE 11. Confocal micrographs illustrating pharyngeal plate and associated structures. A–B in The Weevil Rostrum (Coleoptera: Curculionoidea): Internal Structure And Evolutionary Trends
FIGURE 11. Confocal micrographs illustrating pharyngeal plate and associated structures. A–B, labium and pharyngeal plate in male Arrhenodes minutus (Brentidae: Brentinae). A, ventral aspect; B, dorsal aspect. C, dorsal aspect of pharyngeal plate and mandibles in Sphenophorus sp. (Curculionidae: Dryophthorinae). D–F, mouthparts and pharyngeal plate in Epicaerus imbricatus (Curculionidae: Entiminae). D, ventral aspect; E, lateral aspect; F, dorsal aspect.
Confocal surface texture analysis included in the paper Paixao et al. 2021 - QI. (supplemental to SOM2)
<p>This upload contains all final reports and data of the Confocal surface texture analysis done with ConfoMap and included in the paper Paixao et al. 2021. The Middle Paleolithic Ground Stones Tools of Nesher Ramla Unit V (Southern Levant): a multi-scale use-wear approach for assessing the assemblage functional variability. Quaternary International. (https://doi.org/10.1016/j.quaint.2021.06.009)</p> <p> </p> <p>Pre-print: https://osf.io/gyvw8/</p> <p> </p> <p>Instructions to download all files at once are given here: <a href="https://doi.org/10.5281/zenodo.4011952">https://doi.org/10.5281/zenodo.4011952</a></p>
Confocal micrographs and complete dataset of neuromuscular junction morphology of pelvic limb muscles of the pig (Sus scrofa)
<p>This dataset entails the complete NMJ dataset for three pigs and the three muscles analysed for the publication "Comparative anatomy of the mammalian neuromuscular junction" (https://doi.org/10.1111/joa.13260). This includes spreadsheets (.csv) containing morphometric variables of neuromuscular junction morphology generated using NMJ-morph or aNMJ-morph, as well as muscle fibre diameter (MFD) data for completeness. The three muscles analysed are: extensor digitorum longus (EDL), peroneus longus (PL) and soleus (S). Data contains raw microscope images (.nd2), thresholded and cleaned images of pre- and post-synapse (.tif) and the thresholded and cleaned images of the intermediate muscle endplate (.tif) for the muscle soleus since the "aNMJ-morph" macro saves this intermediate image for measurement of endplate variables.</p> <p>The full data set description is in the readme_file.txt.</p>
FIG. 4 in New insights on the morphology of a digenean parasite Digenea: Brachylaimidae, Brachylaima mazzantii (Travassos, 1927)) using confocal laser scanning microscopy
FIG. 4. — Confocal tomographies of the reproductive system of Brachylaima mazzantii (Travassos, 1927): A, Mehlis' gland (mg), vitelline reservoir (vr), ovary (ov) and testes (t); B, ovary (ov), seminal reservoir (sr), testes (t) and intestinal caeca (ic); C, ovary (ov) and ootype (oo); D, vitelline glands (vg) forming lobed acini; E, vitelline duct (vd) showing vitelline cells inside forming a single row; F, uterus full of eggs; G, egg, revealing the embryo (emb), eggshell (sh), operculum (op) and discontinuity area (da) in the eggshell. Scale bars: A, B, D, F, 50 μm; C, E, 10 μm; G, 5 μm.
FIG. 8 in New insights on the morphology of a digenean parasite Digenea: Brachylaimidae, Brachylaima mazzantii (Travassos, 1927)) using confocal laser scanning microscopy
FIG. 8. — Reproductive system of Brachylaima mazzantii (Travassos, 1927) as first described by Travassos in 1927 (adapted from Lent & Freitas 1937). Scale bar: 1 mm.
FIG. 1 in New insights on the morphology of a digenean parasite Digenea: Brachylaimidae, Brachylaima mazzantii (Travassos, 1927)) using confocal laser scanning microscopy
FIG. 1. — Confocal tomographies of the reproductive system of Brachylaima mazzantii (Travassos, 1927): A, gland cells (gc) surrounding the genital pore (gp); B, commissure (co) and gland cells (gc); C, region of the genital opening showing differentiated musculature (dfm); D, female genital opening (fgo), male genital opening (mgo) and unarmed cirrus (ci); E, cirrus pouch (cip), metraterm (m), testes (t), bursa (b) and seminal vesicle (sv); F, vitelline duct (vd), vitelline reservoir (vr), uterus (u), ovary (ov) and testes (t). Scale bars: 50 μm.
FIG. 6 in New insights on the morphology of a digenean parasite Digenea: Brachylaimidae, Brachylaima mazzantii (Travassos, 1927)) using confocal laser scanning microscopy
FIG. 6. — Confocal tomographies of tegument, musculature of the body and acetabulum of Brachylaima mazzantii (Travassos, 1927): A, tegument covered by many scales; B, scales; C, circular musculature (cm); D, longitudinal (lm) and diagonal musculature (dm); E, two differentiated muscle bundles (dfm); F, surface of acetabulum featuring many papillae (p); G, papillae (p), radial musculature (rm) and differentiated musculature (dfm) supporting the acetabulum; H, papillae. Scale bars: A-G, 50 μm; H, 10 μm.
FIG. 3 in New insights on the morphology of a digenean parasite Digenea: Brachylaimidae, Brachylaima mazzantii (Travassos, 1927)) using confocal laser scanning microscopy
FIG. 3. — Schematic drawings of the reproductive system of Brachylaima mazzantii (Travassos, 1927): A, reconstruction of the reproductive system from the confocal tomographies, showing seminal vesicle (sv), metraterm (m), cirrus (c), cirrus pouch (cp), genital atrium (ga), testes (t), ovary (o), ootype (oo), vitelline duct (vd), vitelline glands (vg) vitelline reservoir (vr), and Mehlis' gland (mg); B, cirrus pouch as first described by Travassos in 1927 (adapted from Lent & Freitas 1937). Scale bars: A, 0.06 mm; B, 0.25 cm.
FIG. 5 in New insights on the morphology of a digenean parasite Digenea: Brachylaimidae, Brachylaima mazzantii (Travassos, 1927)) using confocal laser scanning microscopy
FIG. 5. — Confocal tomographies showing the anterior region of Brachylaima mazzantii (Travassos, 1927): A, image showing the meridional musculature (mm); B, equatorial musculature (eqm); C, radial musculature (rm), papillae (p) on the surface of the oral sucker and differentiated musculature (dfm) making the transition between mouth and pharynx (pre-pharynx); D, pharynx (ph), radial musculature (rm), esophagus (e), and intestinal caeca (ic); E, detail of the intestinal caeca, revealing numerous microvilli (mi), and the epithelium (ep); F, esophageal glands (eg) circling the esophagus. Scale bars: A-D, 50 μm; E, 10 μm.
FIG. 2 in New insights on the morphology of a digenean parasite Digenea: Brachylaimidae, Brachylaima mazzantii (Travassos, 1927)) using confocal laser scanning microscopy
FIG. 2. — Schematic drawings of the genital atrium of Brachylaima mazzantii (Travassos, 1927): A-D, sequential tomographic images starting from the body surface. Scale bar: 5 µm.
FIG. 7 in New insights on the morphology of a digenean parasite Digenea: Brachylaimidae, Brachylaima mazzantii (Travassos, 1927)) using confocal laser scanning microscopy
FIG. 7. — Confocal tomographies of the excretory and nervous system of Brachylaima mazzantii (Travassos, 1927): A, excretory ducts (exd), testes (t); B, excretory bladder (exb), excretory pore (exp), and testes (t); C, longitudinal nervous cord (nc); D, commissures (co) originated from the nervous cord (nc). Scale bars: A-C, 50 μm; D, 10 μm.
FIG. 8. Laser confocal microscopic images. A. Lipokophila eberhardi, female abdomen showing copulatory tubes. B in New genera and species of Plokiophilidae from Australia, Fiji, and Southeast Asia, with a revised classification of the family (Insecta: Heteroptera: Cimicoidea)
FIG. 8. Laser confocal microscopic images. A. Lipokophila eberhardi, female abdomen showing copulatory tubes. B. Heissophila macrotheleae, female abdomen, showing large asymmetrical "vagina" and absence of copulatory tubes. Abbreviations: ct, copulatory tube; vg, vagina (bursa copulatrix).
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>
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.