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15 results for “immunofluorescence imaging”
Spatiotemporal multiplexed immunofluorescence imaging of living cells and tissues with bioorthogonal cycling of fluorescent probes
<p>Raw multichannel and/or Z-stack source data from time series images in TIF format to accompany publication of:</p> <p><strong>Spatiotemporal multiplexed immunofluorescence imaging of living cells and tissues with bioorthogonal cycling of fluorescent probes</strong></p> <p>Jina Ko<sup>1</sup>, Martin Wilkovitsch<sup>2</sup>, Juhyun Oh<sup>1</sup>, Rainer Kohler<sup>1</sup>, Evangelia Bolli<sup>1,3</sup>, Mikael J. Pittet<sup>1,3,4,5</sup>, Claudio Vinegoni<sup>1</sup>, David B. Sykes<sup>6,7</sup>, Hannes Mikula<sup>2</sup>, Ralph Weissleder<sup>1,8</sup>*, Jonathan C. T. Carlson<sup>1,7</sup>*</p> <p><sup>1 </sup>Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge St, CPZN 5206, Boston, MA 02114 </p> <p><sup>2</sup> Institute of Applied Synthetic Chemistry, TU Wien, 1060 Vienna, Austria </p> <p><sup>3</sup> Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland</p> <p><sup>4</sup> Ludwig Institute for Cancer Research, Lausanne Branch, Switzerland</p> <p><sup>5</sup> AGORA Cancer Center, Lausanne, Switzerland</p> <p><sup>6</sup> Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA</p> <p><sup>7 </sup>Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA</p> <p><sup>8 </sup>Department of Systems Biology, Harvard Medical School, 200 Longwood Ave, Boston, MA 02115</p>
hiPSC 3D immunofluorescence images, test data set 2x2, 10Z
<p>Example dataset of human induced pluripotent stem cells, imaged at 40x magnification with a Yokogawa CV7000. This is a small subset of a larger experiment intended as a test dataset for Fractal: https://github.com/fractal-analytics-platform/fractal</p> <p>3 Channels were imaged:</p> <p>- C01: DAPI, nuclear stain</p> <p>- C02: nanog, antibody staining with Bio-Techne AG, AF1997-SP, Lot KKJ0617121 for the stemness marker nanog</p> <p>- C03: Lamin B1, antibody staining with Abcam, ab16048, Lot GR3244890-2 for the nuclear envelope marker Lamin B1</p> <p> </p> <p>This dataset contains 10 Z levels for 4 field of views for those 3 channels, as well as (manually adjusted) metadata files from the Yokogawa CV7000.</p> <p> </p> <p>The data was acquired in the Pelkmans lab in August 2020. The images have been converted from TIFF into PNG (lossless). </p>
OME-Zarr hiPSC 3D immunofluorescence images, tiny test set
<p><em>This dataset is intended to be used for automated testing of OME-Zarr processing.</em></p> <p> </p> <p>Example dataset of human induced pluripotent stem cells, imaged at 40x magnification with a Yokogawa CV7000. This is a tiny subset of a larger experiment intended as a test dataset for the <a href="https://fractal-analytics-platform.github.io/">Fractal platform</a> and others experimenting with OME-Zarrs.</p> <p>1 Channel is included:</p> <ul> <li>C01: DAPI, nuclear stain</li> </ul> <p>It is generated from this raw data: <a href="../records/8287221">https://zenodo.org/records/8287221</a></p> <p>This dataset contains 2 Z levels for 2 field of views for this 1 channel, as well as (manually adjusted) metadata files from the Yokogawa CV7000. The data was acquired in the Pelkmans lab in August 2020.</p> <p>The images have been processed using Fractal, the workflow is attached as a json file. It ran with fractal-server==2.3.6, fractal-client==2.0.1, fractal-web==1.4.0 and fractal-tasks-core==1.2.1.</p> <p>Two versions of the OME-Zarr are added here: A 3D version with both Z planes. And a 2D version (MIP of the Z-planes) which also contains label images from cellpose segmentation, measurements and output ROI tables.</p>
Literature Datasets for the publication "Systematic Review: Prevalence and Practices of Immunofluorescent Cell Image Processing"
<p>This dataset contains the CSV files returned from PubMed searches used to complete a Systematic Review of Image Processing Publication Practices for methods applied to immunofluorescent images of all CNS cells. <br> <br> The file names are organized "date_supplementarytablenumber" followed by the appropriate search terms. </p>
hiPSC 3D immunofluorescence images, tiny test set
<p>Example dataset of human induced pluripotent stem cells, imaged at 40x magnification with a Yokogawa CV7000. This is a tiny subset of a larger experiment intended as a test dataset for Fractal: https://github.com/fractal-analytics-platform/fractal</p> <p>It is a subset of this dataset: https://zenodo.org/record/7057076</p> <p>1 Channel is included:</p> <p>- C01: DAPI, nuclear stain</p> <p> </p> <p>This dataset also contains a small Fractal workflow for standard processing</p> <p> </p> <p>This dataset contains 2 Z levels for 2 field of views for this 1 channel, as well as (manually adjusted) metadata files from the Yokogawa CV7000.</p> <p> </p> <p>The data was acquired in the Pelkmans lab in August 2020. The images have been converted from TIFF into PNG (lossless). </p>
Multi-modal image analysis for large scale cancer tissue studies within IMMUcan: multiplex immunofluorescence images
<p>In cancer research, multiplexed imaging has enabled the in-depth characterization of the tumor microenvironment (TME) and how it relates to patient prognosis. However, standardized, multi-modal data from large numbers of patients to identify robust biomarkers is missing. To provide such data across five cancer indications, the IMMUcan consortium performs broad molecular and cellular spatial profiling of thousands of cancer samples. Two reproducible and scalable workflows have been developed for whole slide multiplexed immunofluorescence (mIF) and imaging mass cytometry (IMC) to overcome challenges of reproducibility and scalability. For mIF we developed IFQuant, a web-based tool optimized for user-friendliness and reproducibility. This Zenodo record contains the mIF images and IFQuant settings to reproduce the results presented in the referenced publication. The companion IMC dataset is available as a joint Zenodo record.</p>
Dual-modality imaging of immunofluorescence and imaging mass cytometry for high-resolution whole slide imaging with accurate single-cell segmentation
<p>Imaging mass cytometry (IMC) is a powerful multiplexed tissue imaging technology that allows simultaneous detection of more than 30 makers on a single slide. It has been increasingly used for single-cell based spatial phenotyping in a wide range of samples. However, it only acquires a small, rectangle field of view (FOV) with a low image resolution that hinders downstream analysis. Here, we reported a highly practical dual-modality imaging method that combines high-resolution immunofluorescence (IF) and high-dementional IMC on the same tissue slide. Our computational pipeline uses the whole slide image (WSI) of IF as spatial reference, integrates small FOV IMC into a WSI of IMC. The high-resolution IF images enable accurate single-cell segmentation to extract robust high-dimensional IMC features for downstream analysis. We applied this method in esophageal adenocarcinoma of different stages, identified the single-cell pathology landscape via reconstruction of WSI IMC images and demonstrated the advantage of the dual-modality imaging strategy.</p>
Fluorescence images of ybx1 mutant neuromasts [Ybx1 immunofluorescence]
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msiFlow: Automated Workflows for Reproducible and Scalable Multimodal Mass Spectrometry Imaging and Immunofluorescence Microscopy Data Processing and Analysis
<p>This record contains example and result data of msiFlow.</p> <p>msiFlow is a collection of automated workflows for reproducible and scalable multimodal mass spectrometry imaging (MSI) and immunofluorescence microscopy (IFM) data processing and analysis. Using an experimental mouse model for urinary tract infection, induced by uropathogenic E.coli (UPEC), we generated data by</p> <ul> <li>matrix-assisted laser desorption ionisation mass spectrometry imaging with laser-induced postionisation (MALDI-2 MSI) using the Bruker timsTOFfleX instrument</li> <li>transmission-mode MALDI-2 MSI (t-MALDI-2)</li> <li>immunofluorescence microscopy (IFM) using the MACSima system from Miltenyi </li> </ul> <p>msiFlow was tested on MALDI-2 MSI, t-MALDI-2 MSI and IFM data of control and UPEC-infected mouse bladder sections. In IFM we used Ly6G and actin for staining neutrophils and the muscle layer. We validated msiFlow on MALDI MSI data of bone marrow (BM)-derived neutrophils. Tentative lipid annotations were validated by MALDI DDA MSI and MALDI MS/MS. All data used and results generated by msiFlow are included in this dataset (besides the intermediate results of the MALDI-2 preprocessing due to data size).</p> <p>The dataset contains the following zip files:</p> <table> <tbody> <tr> <td><strong>zip file</strong></td> <td><strong>description</strong></td> </tr> <tr> <td>ly6g_heterogeneity.zip</td> <td>example and result data (Ly6G clusters) for molecular_heterogeneity_flow</td> </tr> <tr> <td>if_segmentation.zip</td> <td>example and result data (Ly6G segmentation) for if_segmentation_flow</td> </tr> <tr> <td>ly6g_heterogeneity_signatures.zip</td> <td>example and result data (lipids for Ly6G clusters) for molecular_signatures_flow</td> </tr> <tr> <td>ly6g_molecular_signatures.zip</td> <td>example and result data (lipids for Ly6G) for molecular_signatures_flow</td> </tr> <tr> <td>msi_if_registration.zip</td> <td>example and result data for msi_if_registration_flow</td> </tr> <tr> <td>msi_segmentation.zip</td> <td>example and result data (segmented MSI bladder data) for msi_segmentation_flow</td> </tr> <tr> <td>region_group_analysis.zip</td> <td>example and result data (regulated lipids in different bladder tissue regions) for region_group_analysis_flow</td> </tr> <tr> <td>macsima.zip</td> <td>raw IFM data of UPEC-infected bladders containing Ly6G, actin and autofluorescence images</td> </tr> <tr> <td>maldi-bm-neutrophils.zip</td> <td>raw and pre-processed MALDI MSI data of BM-derived neutrophils</td> </tr> <tr> <td>t-maldi-2.zip</td> <td>raw t-MALDI-2 MSI data of a UPEC-infected bladder section</td> </tr> <tr> <td>maldi-2-<em>group-sampleno</em>.zip</td> <td>raw MALDI-2 MSI data of a control/UPEC bladder section</td> </tr> <tr> <td>MALDI_DDA_MSI.zip</td> <td>raw MALDI MSI data acquired in DDA mode</td> </tr> <tr> <td>TIMS_MS_MS.zip</td> <td>raw MALDI TIMS MS/MS data</td> </tr> </tbody> </table> <p> </p>
Immunofluorescence images related to Figure 3A-B
<p>This dataset includes the native images obtained after immunofluorescence against myosin heavy chain and alpha-actinin on myotubes derived from hiPSCs in which the DMD gene was mutated with CRISPR Cas9. Images were acquired with a Nikon A1 RSi confocal microscope and a 20x objective. The .nd2 format can be opened with standard image processing softwares, such as the open source and free software imageJ, available here: https://imagej.nih.gov/ij/download.html, or the QuPath software, available here: https://qupath.github.io/</p>
High-content imaging, immunoblot and immunofluorescence data related to: Caprin-1 binding to the critical stress granule protein G3BP1 is influenced by pH
G3BP is the central node within stress-induced protein–RNA interaction networks known as stress granules (SGs). The SG-associated proteins Caprin-1 and USP10 bind mutually exclusively to the NTF2 domain of G3BP1, promoting and inhibiting SG formation, respectively. Herein, we present the crystal structure of G3BP1-NTF2 in complex with a Caprin-1-derived short linear motif (SLiM). Caprin-1 interacts with His-31 and His-62 within a third NTF2-binding site outside those covered by USP10, as confirmed using biochemical and biophysical-binding assays. Nano-differential scanning fluorimetry revealed reduced thermal stability of G3BP1-NTF2 at acidic pH. This destabilization was counterbalanced significantly better by bound USP10 than Caprin-1. The G3BP1/USP10 complex immunoprecipated from human U2OS cells was more resistant to acidic buffer washes than G3BP1/Caprin-1. Acidification of cellular condensates by approximately 0.5 units relative to the cytosol was detected by ratiometric fluorescence analysis of pHluorin2 fused to G3BP1. Cells expressing a Caprin-1/FGDF chimera with higher G3BP1-binding affinity had reduced Caprin-1 levels and slightly reduced condensate sizes. This unexpected finding may suggest that binding of the USP10-derived SLiM to NTF2 reduces the propensity of G3BP1 to enter condensates.
High-content imaging, immunoblot and immunofluorescence data related to: Caprin-1 binding to the critical stress granule protein G3BP1 is influenced by pH
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STED immunofluorescence imaging of histone protein H3K27 in a 2-cell stage mice embryo
<p>In either confocal or STED mode, immunofluorescence was performed as previously described in [1], using an upright Zeiss microscope with a mounted STEDYCON module and a Zeiss 100x 1.46 NA objective. Primary antibodies used were anti-H3K27ac (Active Motif, 39034) and anti-H3K27me3 (Abcam, ab6002), both at 1:200 dilution. Secondary anti-mouse and anti-rabbit antibodies used were labeled with STAR Red (Sigma-Aldrich, 52283) and STAR Orange (Sigma-Aldrich, 41367), respectively. Excitation was provided by 640 nm (@3%) and 775 nm (@96.5%) lasers for the STAR Red channel, whereas 561 nm (@7.8%) and 775 nm (@100%) lasers were used for the STAR Orange channel. Imaging of the samples was performed with 5 µs pixel dwell time, 64 µm pinhole aperture, 15-line accumulations and a pixel size of 20 nm.</p> <p>Experimental procedures were approved by the EMBL Rome Animal Facility in accordance with European and Italian legislations.</p> <p>1. Bošković, A., Bender, A., Gall, L., Ziegler-Birling, C., Beaujean, N., & Torres-Padilla, M.-E. Analysis of active chromatin modifications in early mammalian embryos reveals uncoupling of h2a.z acetylation and h3k36 trimethylation from embryonic genome activation. Epigenetics 7, 747–757 (2012).</p>
Immunofluorescence images: Inflammasome activation leads to cDC1-independent cross-priming of CD8 T cells by epithelial cell derived antigen
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The datasets for Precise immunofluorescence canceling enables highly multiplexed imaging
<p>Cell states are regulated by responsive signal pathways upon ligand-binding to the receptor and inter-cellular interactions. Thus, high-resolution imaging has been attempted to explore the dynamics of signaling. Recently, multiplexed imaging has been introduced to profile cell state by acquisition of comprehensive spatial protein information in the cells. However, it is still challenging to compromise resolution for visualizing activated signals. Here we developed ‘Precise Emission Canceling Antibody (PECAb)’ attached with erasable fluorescent labeling. PECAbs allow high-resolution sequential imaging using 206 antibodies and it allowed reconstruction of the spatiotemporal dynamics of signaling pathways. Additionally, combining this approach with seq-smFISH can effectively classify cells and identify their signal activation states in human tissue. Overall, the PECAb system serves as a comprehensive platform for analyzing complex cell processes.</p>
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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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.