Find research datasets worth reusing

opencc-by-4.0Apr 2020View details →

Confocal microscopy image stacks from "Temporal integration of auxin information for the regulation of patterning"

This dataset contains raw images in CZI format (Zeiss) of shoot apical meristems (SAM) from Arabidopsis thaliana transgenic lines qDII-pCLV3-pDR5 or qDII-pCLV3-PIN1. See (Galvan-Ampudia and Cerutti et al.) for detailed information. This data constitutes the input of the sam_spaghetti pipeline (<a href="https://gitlab.inria.fr/mosaic/publications/sam_spaghetti">https://gitlab.inria.fr/mosaic/publications/sam_spaghetti</a>) and can be processed using the scripts and examples provided in the package.   File information: File names containing qDII-CLV3-DR5 have the following data: <ul> <li>Channel 1: DII-VENUS-N7</li> <li>Channel 2: pDR5:2xmTurquoise2</li> <li>Channel 3: pRPS5a:TagBFP-SV40</li> <li>Channel 4: pCLV3:mCherry-N7</li> </ul> File names containing qDII-CLV3-PIN1-PI have the following data: <ul> <li>Channel 1: DII-VENUS-N7</li> <li>Channel 2: pPIN1:PIN1-GFP</li> <li>Channel 3: Propidium Iodide (cell walls)</li> <li>Channel 4: pRPS5a:TagBFP-SV40</li> <li>Channel 5: pCLV3:mCherry-N7</li> </ul> Time-lapse sequences are identified as follows: <ul> <li>qDII-CLV3-DR5-E27-LD-SAM7.czi</li> <li>qDII-CLV3-DR5-E27-LD-SAM7-T5.czi</li> <li>qDII-CLV3-DR5-E27-LD-SAM7-T10.czi</li> </ul> where: <ul> <li>qDII-CLV3-DR5 indicates the line</li> <li>E$$-LD (e.g. E25-LD, E27-LD, etc) indicates independent biological replicas</li> <li>SAM$ is the meristem (technical replica)</li> <li>T$ indicates the time elapsed after the first image (in hours)</li> </ul> For example qDII-CLV3-DR5-E27-LD-SAM7-T5.czi is an image of the 7th SAM of the set E27, acquired 5 hours after the first image.

opencc-by-4.0Oct 2023View details →

Confocal image stack of aPKC/FoxP co-staining

Confocal image stacks of whole mount preparations of central nervous systems of adult Drosophila.Genotype: aPKC-Gal4>CD8::GFP, red - FoxP-LexA>CD8::RFP; D: green - D42-Gal4>CD8::GFP, red - FoxP-LexA>CD8::RFP. Confocal image stacks available at:

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Confocal images from: Cell density, alignment, and orientation correlate with C-signal-dependent gene expression during Myxococcus xanthus development

Starving Myxococcus xanthus bacteria use short-range C-signaling to coordinate their movements and construct multicellular mounds, which mature into fruiting bodies as rods differentiate into spherical spores. Differentiation requires efficient C-signaling to drive the expression of developmental genes, but how the arrangement of cells within nascent fruiting bodies (NFBs) affects C-signaling is not fully understood. Here, we used confocal microscopy and cell segmentation to visualize and quantify the arrangement, morphology, and gene expression of cells near the bottom of NFBs at much higher resolution than previously achieved. We discovered that "transitioning cells" (TCs), intermediate in morphology between rods and spores, comprised 10 to 15% of the total population. Spores appeared midway between the center and the edge of NFBs early in their development and near the center as maturation progressed. The developmental pattern as well as C-signal-dependent gene expression in TCs and spores were correlated with cell density, the alignment of neighboring rods, and the tangential orientation of rods early in the development of NFBs. These dynamic radial patterns support a model in which the arrangement of cells within the NFBs affects C-signaling efficiency to regulate precisely the expression of developmental genes and cellular differentiation in space and time. Developmental patterns in other bacterial biofilms may likewise rely on short-range signaling to communicate multiple aspects of cellular arrangement, analogous to juxtacrine and paracrine signaling during animal development.

opencc-zeroOct 2021View details →

opencc-by-4.0Dec 2021View details →

Raw confocal imaging and FRAP data for "Tuning levels of low-complexity domain interactions to modulate endogenous oncogenic transcription"

Raw confocal imaging and FRAP data of "Tuning levels of low-complexity domain interactions to modulate endogenous oncogenic transcription" Shasha Chong1, Thomas G.W. Graham2, Claire Dugast-Darzacq2,5, Gina M. Dailey2, Xavier Darzacq2,5, Robert Tjian2,3,4,5* 1 Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA 2 Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA. 3 Howard Hughes Medical Institute, University of California, Berkeley, CA, USA. 4 Li Ka Shing Center for Biomedical & Health Sciences, University of California, Berkeley, CA, USA. 5 CIRM Center of Excellence, University of California, Berkeley, CA.  * Lead contact Overview This repository contains 1) raw three-color confocal fluorescence images of a transiently expressed protein (mNeonGreen-EWS, mNeonGreen, EGFP-TAF15, EGFP, mNeonGreen-EWS-NPM1, or mNeonGreen-NPM1), endogenously expressed EWS::FLI1-Halo labeled with JFX549 Halo ligand, and intron RNA fluorescence in situ hybridization (FISH) targeting ABHD6, CAV1, or GAPDH in genome-edited A673 cells, 2) raw fluorescence recovery after photobleaching (FRAP) movies of endogenously expressed EWS::FLI1-Halo labeled with TMR Halo ligand in genome-edited A673 cells in the presence and absence of transient expression of mNeonGreen-EWS-NPM1. The imaging data, after being processed, were used to generate Figure 1D-G (also S1A, S3, and S4), 2E-G (also S5A and S7), 3C-E (also S9), 4A, S2, S6, and S8 of the manuscript in the title.  Method details 1. RNA fluorescence in situ hybridization (FISH) The genome-edited A673 cells (described in https://www.science.org/doi/10.1126/science.aar2555) were plated on 18 mm circular No. 1 cover glasses (VWR VistaVision, 16004-300) and transfected with a protein expression plasmid using Lipofectamine 3000. 24 hours after transfection, we stained the cells with 200 nM JFX549 HaloTag ligand following the protocol described above, fixed the cells, and then proceeded with RNA FISH. To measure nascent transcription levels of ABHD6, CAV1, and GAPDH genes, we performed intron RNA FISH following the published Stellaris RNA FISH protocol for adherent cells (https://biosearchassets.blob.core.windows.net/assets/bti_stellaris_protocol_adherent_cell.pdf) using Quasar 670-labeled FISH probes designed with the online software Stellaris Probe Designer (https://www.biosearchtech.com/support/tools/design-software/stellaris-probe-designer) and purchased from LGC Biosearch Technologies.  2. Confocal fluorescence imaging of protein and nucleic acid distribution Two confocal microscopes were used to image intron RNA FISH samples. One is an inverted laser scanning confocal microscope (Zeiss, LSM 710 AxioObserver) equipped with 34-channel spectral detection, a motorized stage, a full incubation chamber maintaining 37°C and 5% CO2, a heated stage, an X-Cite 120 illumination source as well as several laser lines (405, 458, 488, 514, 561, 591, 633 nm). Images were acquired with a 40x Plan NeoFluar NA1.3 oil-immersion objective under control of the Zeiss Zen software. The other is an inverted laser scanning confocal microscope with Airyscan super-resolution capability (Zeiss, LSM 900 with Airyscan 2) and equipped with four laser lines (405, 488, 561, 640 nm). Images were acquired with a 40x oil objective (Zeiss Plan-Apochromat 40x/1.3 Oil DIC) in the confocal (CO) mode under control of the Zen software. We acquired z stacks of RNA FISH samples with a slice interval of 0.3 mm. 405 nm, 488 nm, 561 nm, and 633 or 640 nm lasers were used to excite the fluorescence of Hoechst-labeled nuclei, EGFP or mNeonGreen-labeled proteins, JFX549-labeled EWS::FLI1-Halo, and Quasar 670-labeled intron RNA FISH, respectively. Before acquiring any fluorescence image, we carefully set the laser intensity and microscope detectors to make sure that no pixel in the image was saturated. We used proper emission filters for sequential four-color imaging and ensured no bleed-through between the four channels by imaging cell samples that contain only one of the four fluorophores (Hoechst, EGFP or mNeonGreen, JFX549, and Quasar 670) under the four-color imaging settings. 3. Fluorescence recovery after photobleaching (FRAP) FRAP was performed on the inverted laser scanning confocal microscope (Zeiss, LSM 710 AxioObserver) described above. The 561 nm laser and the epi-illumination mode were used for FRAP measurements. Images were acquired with a 40x Plan NeoFluar NA1.3 oil-immersion objective. The knock-in A673 cells were grown on glass-bottom (No. 1.5, 14 mm diameter) 35 mm dishes (MatTek, P35G-1.5-14-C). To measure the FRAP dynamics of EWS::FLI1-Halo in the nucleolus, we transfected the knock-in cells with a plasmid encoding mNG-EWS-NPM1 and stained the cells with 500 nM HaloTag TMR ligand (Promega, G8251) following the protocol described above. We acquired 1000 frames at one frame per 0.3 seconds with the first 5 frames acquired before the bleach pulse for the measurement of baseline fluorescence of the bleach spot and the whole nucleus. We chose to photobleach a circular spot with a radius of 1 μm within a nucleolus using the 561 nm laser at maximum intensity. To measure the FRAP dynamics of EWS::FLI1-Halo in the nucleoplasm, we followed the same procedure as above, except that the knock-in cells were not transfected and a circular bleach spot with a radius of 1 μm was chosen within the nucleoplasm of a cell and at least 1 μm from nuclear and nucleolar boundaries.

opennotspecifiedDec 2017View details →

Fig. 2 Confocal laser scanning microscopy images showing the hard tick morphology. a in parasitised feathered dinosaurs as Cretaceous amber assemblages revealed

Fig. 2 Confocal laser scanning microscopy images showing the hard tick morphology. a Habitus in ventral view of the Cornupalpatum burmanicum nymph associated with feathers. Scale bar, 0.2 mm. b Detail of the gnathosoma and coxal area in ventral view revealing the absence of genital pore. Scale bar, 0.1 mm. c Dorsal view detail of the gnathosoma and anterior part of the scutum (arrow indicates the lateral margin of the scutum). Scale bar, 0.1 mm

opencc-by-4.0May 2024View details →

Raw Confocal Images for "A quantitative gibberellin signaling biosensor reveals a role for gibberellins in internode specification at the shoot apical meristem"

Abstract: Growth at the shoot apical meristem (SAM) is essential for shoot architecture construction. The phytohormones gibberellins (GA) play a pivotal role in coordinating plant growth, but their role in the SAM remainsmostly unknown. Here, we developed a ratiometric GA signaling biosensor by engineering one of the DELLA proteins, to suppress its master regulatory function in GA transcriptional responses while preserving its degradation upon GA sensing. We demonstrate that this degradation-based biosensor accurately reports on cellular changes inGA levels and perception during development.Weused this biosensor to map GA signaling activity in the SAM. We show that high GA signaling is found primarily in cells located between organ primordia that are the precursors of internodes. By gain- and loss-of-function approaches, we further demonstrate that GAs regulate cell division plane orientation to establish the typical cellular organization of internodes, thus contributing to internode specification in the SAM.

opencc-by-4.0Oct 2022View details →

The raw images of Laser Confocal Microscopy experiments in the manuscript: Inert Pepper aptamer-mediated endogenous mRNA recognition and imaging in living cells

The original imaging data folder contains the raw images of Laser confocal microscopy experiments in the manuscript: Inert Pepper aptamer-mediated endogenous mRNA recognition and imaging in living cells. <a href="https://doi.org/10.1093/nar/gkac368">https://doi.org/10.1093/nar/gkac368</a>

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 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-4.0Aug 2023View details →

On the risk of manual annotations in 3D confocal microscopy image segmentation

This dataset contains different annotated masks of human induced pluripotent stem cell nuclei from the dataset published with https://doi.org/10.1038/s41586-022-05563-7 and DL models trained using these masks. Napari-GT and Slicer-GT were manually annotated using the Napari and 3D Slicer software considering only the DNA channel, while for bioGT the Lamin B1 channel was annotated using the seeded watershed algorithm to obtain a reproducible and biologically plausible nucleus annotation. This dataset is provided to reproduce the results in the manuscript "On the risk of manual annotations in 3D confocal microscopy image segmentation", more details can be found there.

closedIPD-NOFeb 2026View details →

Ex-vivo Confocal Imaging and Proteomic Profiling to Determine Treatment Response in Children With IBD

ClinicalTrials.gov study NCT07121920. IPD Sharing: NO. Countries: 1. Publications: 14.

Fibered Confocal Fluorescence Microscopy Imaging in Patients With Diffuse Parenchymal Lung Diseases

ClinicalTrials.gov study NCT01624753. IPD Sharing: Not stated. Countries: 1. Publications: 4.

Fundus Autofluorescence Imaging in Age-related Macular Degeneration Using Confocal Scanning Laser Ophthalmoscopy

ClinicalTrials.gov study NCT00393692. IPD Sharing: UNDECIDED. Countries: 1. Publications: 25.

closedIPD-NOFeb 2026View details →

Confocal Laser Endomicroscopy as an Imaging Biomarker for the Diagnosis of Pancreatic Cystic Lesions

ClinicalTrials.gov study NCT03492151. IPD Sharing: NO. Countries: 1. Publications: 1.

In Vivo Imaging of Pigmentary Disorders by Reflectance Confocal Microscopy

ClinicalTrials.gov study NCT00771355. IPD Sharing: Not stated. Countries: 1. Publications: 1.

Confocal Probe-based Endoscopic Imaging, Colorectal Cancer, Gastrointestinal (GI) Pathologies

ClinicalTrials.gov study NCT00874263. IPD Sharing: Not stated. Countries: 1. Publications: 3.