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13 results for “DAPI”
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
<p>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.</p> <p>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.</p> <p>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.</p>
HeLa-DAPI-EdU488-mCherryH2B
<p>Sample : HeLa cells fixed cells <br> Hyperstack : 3c, 1z, 1t<br> Microscope : Confocal Zeiss 710,<br> Objective : Plan-Aprochromat 40x/1.3 Oil DIC M27<br> Pinhole size : 37 um<br> Pixel size : 0.42 um<br> c1 : DAPI , 405<br> c2 : EdU-Alexa488, 488<br> c3 : mCherry, 555</p> <p>License: CC-BY 4.0, Romain Guiet, BIOP, EPFL</p>
DAPI stained nuclei more or less clustered
<p>DAPI stained nuclei more or less clustered and the corresponding cells stained with TexasRed.</p>
Fig. 4. DAPI and CMA 3 in Identification of distinct evolutionary units in allopatric populations of Hypostomus cf. wuchereri Günther, 1864 (Siluriformes: Loricariidae): karyotypic evidence
Fig. 4. DAPI and CMA 3 stained chromosomal pairs from Mutum (a) and Una (b) Rivers, showing AT and GC-rich sites, respectively. The NOR-bearing pair is highlighted.
Morphological features associated with Dapi and Nissl images from seqFISH and seqFISH+ datasets
<p>To go with the convnet.morpho package from:</p> <p>https://bitbucket.org/qzhudfci/convnet.morpho/src/master/</p> <p>Image data:</p> <p>brain1.images.zip</p> <p>brain2.images.zip</p> <p>seqfishplus.images.zip</p> <p> </p> <p>Alexnet extracted feature vectors (npy):</p> <p>brain1.image.data.zip</p> <p>brain2.image.data.zip</p> <p>seqfishplus.image.data.zip</p> <p> </p>
Fluorescent images of actin and DAPI-labelled MCF10A, MCF7 and MDA-MB-231 cell lines
<p>This dataset of cell images was generated to understand the morphological changes between less and more metastic cancer cells and between normal and cancerous cells. They have been used in the linked publications.</p>
DAPI images, molecules and segmentation boundaries for: A Spatiotemporal Atlas of Mouse Gastrulation and Early Organogenesis to Explore Axial Patterning and Project In Vitro Models onto In Vivo Space
<div> </div> <p><strong>Data Description</strong></p> <ol> <li><strong>Stitched & rotated DAPI images</strong> - tiff file format filename indicates sample and optical z-slice position, i.e. embryo3_z5.tif is the DAPI image for embryo 3 in optical z-slice 5. Also provided in PNG format.</li> <li><strong>Detected molecules and cell segmentation in MoleculeExperiment objects</strong> - RDS files to read data using the MoleculeExperiment format in R/Bioconductor. Filename embryo3_z5.Rds indicates MoleculeExperiment RDS file for embryo 3 in optical z-slice 5. Coordinates are provided in microns. Note that z-slices 2 and 5 are only provided for embryos 1,2,3 as they were originally provided in Lohoff et al, Nature Biotechnology, 2023.</li> <li><strong>Pixels-to-microns conversion</strong> - pixelSize.R Simple R script/text to indicate the size of each pixel in the DAPI images, this is to align the coordinate systems between the DAPI images and molecules.<br><br> <div> <h4>Project Abstract</h4> </div> <p>At the onset of murine gastrulation, pluripotent epiblast cells migrate through the primitive streak, generating mesodermal and endodermal precursors, while the ectoderm arises from the remaining epiblast. Together, these germ layers establish the body plan, defining major body axes and initiating organogenesis. Although comprehensive single cell transcriptional atlases of dissociated mouse embryos across embryonic stages have provided valuable insights during gastrulation, the spatial context for cell differentiation and tissue patterning remain underexplored. In this study, we employed spatial transcriptomics to measure gene expression in mouse embryos at E6.5 and E7.5 and integrated these datasets with previously published E8.5 spatial transcriptomics and a scRNA-seq atlas spanning E6.5 to E9.5. This approach resulted in a comprehensive spatiotemporal atlas, comprising over 150,000 cells with 88 refined cell type annotations as well as genome-wide transcriptional imputation during mouse gastrulation and early organogenesis. The atlas facilitates exploration of gene expression dynamics along anterior-posterior and dorsal-ventral axes at cell type, tissue, and organismal scales, revealing insights into mesodermal fate decisions within the primitive streak. Moreover, we developed a bioinformatics pipeline to project additional scRNA-seq datasets into a spatiotemporal framework and demonstrate its utility by analysing cardiovascular models of gastrulation3. To maximise impact, the atlas is publicly accessible via a user-friendly web portal empowering the wider developmental and stem cell biology communities to explore mechanisms of early mouse development in a spatiotemporal context.</p> </li> </ol>
DAPI stained Gonatus onyx retina
<p>(a) DAPI stained transverse cross-section of juvenile G. onyx (15mm ML) eye. Nuclei appear blue. (b) Enlarged section of b’ de-picting retinal layers. (c) Enlarged section of c’ depicting the iris. (d) Enlarged section of d’ depicting the transition from the retina to the ciliary body, and view of the cartilaginous part of the sclera. Abbreviations: dorsal (do), ventral (ve), posterior (po), anterior (an), inner segment of photoreceptor (isp), basal membrane (bm), supporting cells (sc), outer segment of photoreceptor (osp), limiting membrane (lm), sclera (s). </p>
Fluorescent images of actin and DAPI-labelled MCF10A, MCF7 and MDA-MB-231 cell lines
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Human and mouse ALS tissue sections immunolabeled for FUS, SFPQ, ChAT and counterstained with DAPI
<p>Raw images and image processing scripts to reproduce results of the manuscript entitled 'Human and mouse ALS tissue sections immunolabeled for FUS, SFPQ, ChAT and counterstained with DAPI' and posted on BioRxiv in August 2020.</p> <p><strong>1. RowMouseImages.zip</strong></p> <p>Tissue sections from spinal cord of SOD1- and VCP-mutant ALS mouse models together with control immunolabeled for FUS, SFPQ, ChAT and counterstained with DAPI.</p> <p><strong>2. HumanMouseImages.zip</strong></p> <p>Tissue sections from spinal cord of Healthy and sporadic ALS donors immunolabeled for FUS or SFPQ, ChAT and counterstained with DAPI.</p> <p><strong>3. ImageProcessingScripts.zip</strong></p> <p>Scripts to preprocess these images.</p> <p><strong>4. Data.zip</strong></p> <p>CSV files of the single-cell measurements obtained from CellProfiler after segmentation as presented in ImageProcessingScripts.zip. Downstream analysis leading to automatic identification of MNs subpopulation can be acessed on Github <a href="https://github.com/RLuisier/ALSdisMNs">https://github.com/RLuisier/ALSdisMNs</a></p> <p>---------</p> <p>The two series of multichannel fluorescent microscopy data have been used in several manuscripts including:</p> <ol> <li><strong><a href="http://paperpile.com/b/Jw7dut/7eYh">Luisier R, Tyzack GE, Hall CE, Mitchell JS, Devine H, Taha DM, et al. Intron retention and nuclear loss of SFPQ are molecular hallmarks of ALS. Nat Commun 2018; 9: 2010.</a></strong></li> <li><strong><a href="http://paperpile.com/b/Jw7dut/SxxR">Tyzack GE, Luisier R, Taha DM, Neeves J, Modic M, Mitchell JS, et al. Widespread FUS mislocalization is a molecular hallmark of amyotrophic lateral sclerosis. Brain 2019; 142: 2572–80.</a></strong></li> </ol> <p> </p>
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
<p>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.</p> <p>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.</p> <p>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.</p>
DAPI and Phase Contrast Images Dataset
<p>Data was acquired on an Olympus IX83 microscope using a 20x/0.4 Ph2 Objective.</p> <p>Kohler illimination was established before acquistion started.</p> <p>Sample consists of cultured HeLa Cells on #1.5 (170 um) coverslips, 12mm diameter.</p> <p> </p> <p>A single coverlsip was imaged in a 10x10 grid with no overlap (total: 100 images)</p> <p>Each image was acquired sequentially in</p> <ul> <li><strong>Phase Contrast</strong> (50ms exposure time, using a 535nm LED)</li> <li><strong>DAPI</strong> 100 ms exposure time</li> </ul>
Data from: Karyotype analysis of Panax ginseng C.A. Meyer, 1843 (Araliaceae) based on rDNA loci and DAPI band distribution
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