Find research datasets worth reusing

opencc-by-4.0Mar 2024View details →

Correlative microscopy of mice cerebellar Purkinje cells from 20x confocal tissue imaging to super-resolution 93x 3D STED of dendritic spines

This Dataset concerns the paper entitled "From tissues to segmentation: a modular framework for multi-scale neuron isolation" by Cauzzo et al. Nature Comm (2024). S.Cauzzo$, E. Bruno, D. Boulet, P. Nazac, M. Basile, A. L. Callara, F. Tozzi, A. Ahluwalia, C. Magliaro, L. Danglot$*, N. Vanello$*    *shared senior authorship: Lydia.danglot@inserm.fr ; nicola.vanello@unipi.it $ corresponding authors : cauzzo.simone@gmail.com  ; Lydia.danglot@inserm.fr ; nicola.vanello@unipi.it

opencc-by-4.0Nov 2024View details →

Widefield and Confocal brain images derived from experimental Middle Cerebral Artery occlusion (MCAo) in mice.

This deposit contains a series of widefield and confocal brain images derived from research on cerebral ischemia carried out by the Laboratory of Neurovascular Interactions (https://elalilab.com/) at the Université Laval, Québec (Canada) directed by Dr. Ayman ElAli (<a href="mailto:ayman.el-ali@crchudequebec.ulaval.ca">ayman.el-ali@crchudequebec.ulaval.ca</a>). The experiments, data processing, and organization were performed by Daniel Manrique-Castano, former postdoctoral fellow and current research data curation officer at the Digital Research Alliance of Canada (<a href="https://daniel-manrique.github.io/">https://daniel-manrique.github.io/manrique; </a>dmanriquecastano@gmail.com). Given the complexity of the whole image bundle, images from the same experiment were compressed into zip files. Complementary data is available at the Open Science Framework (OSF) repository (<a href="https://osf.io/74mqn/" target="_blank" rel="noopener">10.17605/OSF.IO/74MQN</a>), and reproducible workflows for image processing and analysis are available on GitHub (<a href="https://doi.org/10.5281/zenodo.13948420" target="_blank" rel="noopener">10.5281/zenodo.13948420</a>)   Naming conventions for datasets (taking as an example Widefield_5x_Ipsilateral_KO_CD31-ColIV-Iba1.zip) Widefield: Imaging type performed (available strings = Confocal, Widefield).  5x: Objective magnification (Available strings = 5x, 10x, 20x, 40x).  Ipsilateral: Iaged region (Available strings = ROIs [Regions of interest], Whole [whole brain], Ipsilateral [ischemic hemisphere]).  KO: imaging performed in PDGFRB_KLF4-KO mice (if absent, imaging performed in PDGFRB_TdTomato mice)  CD31-ColIV-Iba1: Imaged markers (available strings = multiple, depending on the experiment).    Important: Each .zip file contains a README file specific to each dataset, describing the experimental conditions, naming conventions of individual images and links to additional files used for image processing.

opencc-by-4.0Jun 2023View details →

Deconvolved STED nanoscopy images of the nuclear phosphatidylinositol 4,5-bisphosphate and nuclear speckle marker SON together with deconvolved confocal images of DAPI stained nuclei in human formalin-fixed paraffin-embedded skin warts sections

The collection and analysis of formalin-fixed paraffin-embedded (FFPE) human skin sections was approved by the local ethics-committee at the Department of Pathology, University of Cologne, Germany. Written informed consentwas obtained from all patients in accordance with the Declaration of Helsinki. For biopsy materials from archival paraffin blocks of human skin, an informed consent was obtained from all the subjects and ethical approval obtained from the Ethics Committee at the University of Cologne. Surgically removed human FFPE skin biopsies were sectioned into 4 µm sections. Sections were dewaxed, and indirectly immunofluorescently labeled against nuclear phosphatidylinositol 4,5-bisphosphate (nPI(4,5)P2) using  5 µg/mL rabbit primary polyclonal antibody (Echelon Biosciences Inc. Z-A045, clone 2C11). The primary antibody against nPI(4,5)P2 was recognized by the goat secondary antibody conjugated with Abberrior Star 635P (Abberior 2-0002-007-5). Sections were indirectly immunofluorescently labeled against nuclear speckle marker SON using  1 µg/mL rabbit primary polyclonal antibody (Abcam ab121759). The primary antibody against SON was recognized by the goat secondary antibody conjugated with Abberrior Star 580 (Abberrior ST580-1002). Sections were co-stained by DAPI 1:1000 in PBS for 5 min. Imaging of nPI(4,5)P2-635P channel was performed on Leica TCS SP8 STED 3x inverted DMi8 microscope with pulsed white light laser 470-640 nm 1.5 mW and 775 nm pulse STED laser >1.5 W controlled by Leica Application Suite X software and equipped with HC PL APO CS2 100x/1.40 OIL objective used with Leica Type F immersion oil n=1.518. Unidirectional xyz scanning speed was 400 Hz, line accumulation 8. Pixel size was 20 nm in X and Y. Channel settings: 7% 633 nm laser; 775 Notch filter; 50% 775 nm STED laser; 30% 3D STED; HyD 639-698 nm, photon-counting mode, gain 100, gating 0.3-10 ns. Imaging of SON-580 channel was performed on Leica TCS SP8 STED 3x inverted DMi8 microscope with pulsed white light laser 470-640 nm 1.5 mW and 775 nm pulse STED laser >1.5 W controlled by Leica Application Suite X software and equipped with HC PL APO CS2 100x/1.40 OIL objective used with Leica Type F immersion oil n=1.518. Unidirectional xyz scanning speed was 400 Hz, line accumulation 8. Pixel size was 20 nm in X and Y. Channel settings: 10% 585 nm laser; 775 Notch filter; 80% 775 nm STED laser, 30% 3D STED; Hybrid detector (HyD) 589-616 nm, photon-counting mode, gain 100, gating 0.4-10 ns. Z-stacks of STED images were deconvolved using Huygens Professional 22.10 software (Scientific Imaging B.V.). Data sets were processed using Workflow Processor. The workflow consisted of selecting images, setting up the microscopy and deconvolution parameters and saving deconvolved images as 8-bit TIFF single files for individual channels (which were later used for the quantitative analyses; see below). Microscopy parameters were optimized and set as follows. Sampling intervals were ≤20 nm in X and Y and  ≤20 nm in Z. Numerical aperture was 1.4; refractive indexes of the lens immersion oil was 1.518 and of the embedding media 1.458; objective quality was good, coverslip position was 0 µm and imaging direction was downward. For nPI(4,5)P2-635P STED channel the backprojected pinhole was 216 nm; excitation (ex.) and emission (em.) wavelengths (λ) were 633 and 651 nm, resp., ex. fill factor 2. STED depletion mode was pulsed, saturation factor 25, STED λ = 775, STED immunity factor 10 and STED 3X was 30%. Classic MLE algorithm with stabilization of Z-slices was used and signal-to-noise ratio was 5.1. For SON-580 STED channel the backprojected pinhole was 195 nm; excitation (ex.) and emission (em.) wavelengths (λ) were 585 and 602 nm, resp., ex. fill factor 2. STED depletion mode was pulsed, saturation factor 20, STED λ = 775, STED immunity factor 10 and STED 3X was 30%. Classic MLE algorithm with stabilization of Z-slices was used and signal-to-noise ratio was 4.

opencc-by-4.0Oct 2023View details →

Confocal microscopy images of Escherichia coli cells treated with various antibiotics (LB, exponential phase)

This dataset and CARE model is part of the publication "Transertion and cell geometry organize the Escherichia coli nucleoid during rapid growth".It contains all CLSM images that were used for the publication, as well as the single-cell regions of interest for analyses.Cells were grown to exponential phase in LB Lennox and antibiotics were added for 0-60 min. Cultures were then chemically fixed, immobilized and stained for DNA (DAPI) and membrane (Nile Red). The strain (NO34) expresses a MreBsw-sfGFP fusion protein from the native chromosomal locus. It was a kind gift from Zemer Gitai (<a href="http://doi:10.1016/j.bpj.2016.07.017">Ouzounov et al., 2016</a>).More information can be found in the publication.

opencc-by-4.0Feb 2024View details →

Metadata for Confocal Laser Scanning Microscopy Images of Monoculture and Mixed-Species Biofilms Formed by Bacterial Isolates of Dairy Origin

In a project conducted by ILVO (Belgium), a wide variety of bacterial species were recovered from the surface of a dairy pasteurizer after cleaning and disinfection (C&D). The biofilm-forming ability of these bacteria was determined in both single-species and various mixed-culture combinations. Some work related to this study has been published in Frontiers: "Synergistic interactions in multispecies biofilm combinations of bacterial isolates recovered from diverse food processing industries". Bacterial species were mixed in different combinations to assess the community biofilm mass and growth dynamics of individual species. ILVO and the University of Copenhagen conducted experiments aimed at revealing the structural characteristics and spatial organization of bacterial species within different mixed-species biofilms. In our research, we employed oligonucleotide FISH probes, each conjugated with a unique fluorescent dye: Cy5 for Stenotrophomonas rhizophila (B68), Cy3 for Bacillus licheniformis (B65), and FAM for Microbacterium lacticum (B30). C1 combination refers to a combination containing B68 and B30.  Images of the biofilms formed on the coupons were captured using a confocal laser scanning microscope (LSM 800, Zeiss) with a Plan-Apochromat 63x/1.4 oil-immersion objective. Z-stacks were recorded to obtain three-dimensional (3D) images. Standard images were made with an image size of 1024 × 1024 pixels, corresponding to physical dimensions of 101.4 × 101.4 μm for each image. For each image, two separate channels were applied to detect any dual-species combination using a flexible detector (GaAsP-PMT) in the LSM 800 system. Representative 3D views of images were generated using the 3D model function in the ZEN system 3.7. Biofilms were grown in BHI for 24 h on plastic coupons. The samples were imaged at different time points: 6h, 12h, 18h and 24h. Each samples had three replicates and for each replicate imaging was performed from 3-6 different positions.  Details of the oligonucleotide probes are given below: <table> <tbody> <tr> <td> Name of the species </td> <td> Sequences </td> <td> Max. excitation </td> <td> Max. emission </td> <td> Fluorophores </td> </tr> <tr> <td> S. rhizophila B68  </td> <td> GGGCCTTTACCCCGCCA </td> <td> 649 nm </td> <td> 670 nm </td> <td> Cy5 </td> </tr> <tr> <td> B. licheniformis B65 </td> <td> ACCGCCTGCGCGCGCTT </td> <td> 550 nm </td> <td> 570 nm </td> <td> Cy3 </td> </tr> <tr> <td> M. lacticum B30 </td> <td> CCCCACCCTTTCGCTCC </td> <td> 495 nm </td> <td> 520 nm </td> <td> FAM </td> </tr> </tbody> </table>

opencc-by-4.0Apr 2024View details →

Correlative microscopy of rat cultured hippocampal pyramidal cell from 40x confocal imaging to super-resolution 93x 3D STED of dendritic spines

This dataset contain multi-scale image of rat hippocampal pyramidal cell related to our paper "From tissues to segmentation: a modular framework for multi-scale neuron isolation" by Cauzzo et al. Nature Comm (2024).

opencc-by-4.0May 2018View details →

Sparks et al, Heterogeneity in tumor chromatin-doxorubicin binding revealed by in vivo fluorescence lifetime imaging confocal endomicroscopy: In vitro data

Data is divided into three folders: <ul> <li>Sparks_et_al_FIG2_Histone_vs_free_GFP <ul> <li>data for Sparks et al Figure 2</li> <li>main text section: 'FRET between  chromatin-bound GFP and doxorubicin'</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: 'FLIM endomicroscope can monitor doxorubicin cellular uptake'</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> Cell lines IGROV-1 cell lines were cultured in CO2 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. 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. 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. In vitro experiments 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. 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.

opencc-by-4.0May 2018View details →

Sparks et al, Heterogeneity in tumor chromatin-doxorubicin binding revealed by in vivo fluorescence lifetime imaging confocal endomicroscopy: in vivo data

Data is divided into three folders: <ul> <li>Sparks_et_al_FIG_6_IP_intranodule_heterogeneity <ul> <li>data for Sparks et al Figure 6</li> <li>main text section: 'FRET between  chromatin-bound GFP and doxorubicin'</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: 'FLIM endomicroscope can monitor doxorubicin cellular uptake'</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: 'Intra-tumor heterogeneity'</li> </ul> </li> </ul> In vivo experiments 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-1 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. 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.

opencc-by-4.0Feb 2015View details →

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).

opencc-by-4.0Jan 2023View details →

Confocal Microscopy Imaging of Peptidoglycan Uptake in the Mouse Intestine

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 Stainings are described in detail in the the PNAS article methodology. Files names beginning Fig 5A-1; DAPI, WGA, anti-E-cadherin, MDP-rhodamine Files names beginning Fig 5A-2, Fig 5A-3 & Fig S5;  DAPI, Phalloidin, anti-Siglec-F, MDP-rhodamine Files names beginning Fig 5B; DAPI, Phalloidin, E.coli peptidoglycan-Alexa Fluor 647 conjugate Files names beginning Fig 6B; DAPI, Phalloidin, anti-Siglec-F, MDP-rhodamine (also corresponds to Supplementary data Figure 5) Files names beginning Fig S5-1; DAPI, Phalloidin, anti-CgA, MDP-rhodamine Files names beginning Fig S5-2; DAPI, Phalloidin, anti-NKM-16-4-2, MDP-rhodamine

opencc-by-4.0May 2023View details →

Confocal microscopy images (CZI files) of human chondrocytes of different resolutions and magnifications with stained nuclei and primary cilia

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. 1. Methods 1.1 Cell culture 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/cm2 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% CO2 and 5% O2 with different media compositions for three days. 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−1 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−1 insulin-like growth factor (IGF)-1 (R&D Systems, Minneapolis, MN, USA) and 50 ng mL−1 transforming growth factor (TGF)-β1 (Peprotec, Hamburg, Germany). 1.2 Immunocytochemistry 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). 1.3 Image acquisition 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).

opencc-by-4.0May 2023View details →

Confocal microscopy images (CZI files) of human chondrocytes in different cell culture media with stained nuclei and primary cilia

1. Methods 1.1 Cell culture 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/cm2 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% CO2 and 5% O2 with different media compositions for three days. 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−1 ascorbic acid (Sigma-Aldrich, Merck KGaA, Darmstadt, Germany). To this basal medium, different supplements were added, creating four groups: 1) ITS: 1% Insulin-Transferrin-Selenium (ITS+™ Premix, BD Biosciences, Franklin Lakes, NJ, USA), 2) ITS with Dexa: 1% Insulin-Transferrin-Selenium (ITS+™) and 100 nM dexamethasone (Sigma-Aldrich, Merck KGaA, Darmstadt, Germany), 3) ITS with Dexa + IGF-1 + TGF-β1: 1% Insulin-Transferrin-Selenium (ITS+™), 100 nM dexamethasone, 50 ng mL−1 insulin-like growth factor (IGF)-1 (R&D Systems, Minneapolis, MN, USA) and 50 ng mL−1 transforming growth factor (TGF)-β1 (Peprotec, Hamburg, Germany), 4) FBS: 10% fetal bovine serum (FBS, Pan Biotech, Aidenbach, Germany). 1.2 Immunocytochemistry 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). 1.3 Image acquisition 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).

opencc-by-4.0Jan 2021View details →

Super-resolved Reflectance Confocal Microscopy time-lapse imaging of a living MEF cell lamellipod

This movies presents a time-lapse of a label-free living Mouse embryonic fibroblast cell observed with super-resolved rescanned reflectance confocal microscopy..

opencc-by-4.0Mar 2017View details →

Entire confocal z-stack series as .tif image sequences

The manuscript entitled "Parvalbumin-expressing ependymal cells in rostral lateral ventricle wall adhesions contribute to aging-related ventricle stenosis in mice" shows confocal z-stack maximum intensity projections and thin z-plane reconstructions in the figure plates. The entire confocal z-stack image series are provided here as .tif image sequences, respectively the confocal z-stacks of the negative controls as well. The file names refer to the figure numbers and position in the figure plates. For more information about the immunostaining and image acquisition, see the Materials & Methods and Figure legends in the manuscript.

opencc-by-4.0Feb 2024View details →

Source code and data for manuscript "Large-scale deep tissue voltage imaging with targeted illumination confocal microscopy"

Source code and data for manuscript "Large-scale deep tissue voltage imaging with targeted illumination confocal microscopy", Nat Methods (2024), https://doi.org/10.1038/s41592-024-02275-w.

opencc-by-4.0Mar 2022View details →

Confocal images of rDRG neurons overexpressing human GDAP1 and its R120W and H123R variants

Original confocal images for panels in Figure 6 in Sutinen et al. (2022). The images correspond to rDRG primary neurons overexpressing RFP or human GDAP1 (wild-type, R120W, H123R variants). Included is a Zip file with 16 TIFF files, one for each panel.

opencc-by-4.0Jun 2024View details →

Annotated and processed 3D confocal microscopy images of dorsal aorta in wild-type and Endoglin-deficient zebrafish embryos at 48 hpf and 72 hpf

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. 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>. 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>.