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1,317 results for “Histology”
Multiplexed histology of COVID-19 post-mortem lung samples - ACUTE CASE 2 FOV3
<p><strong>Image-based data set of a post-mortem lung sample from a COVID-19 donor (ACUTE CASE 2 FOV3)</strong></p> <p>Each image shows the same field of view (FOV), sequentially stained with the depicted fluorescence-labelled antibodies, including surface proteins, intracellular proteins and transcription factors. Images contain 2024 x 2024 pixels and are generated using an inverted wide-field fluorescence microscope with a 20x objective, a lateral resolution of 325 nm and an axial resolution above 5 µm. Images have been normalized and intensities adjusted.</p>
Multiplexed histology of COVID-19 post-mortem lung samples - ACUTE CASE 1 FOV2
<p><strong>Image-based data set of a post-mortem lung sample from a COVID-19 donor (ACUTE CASE 1 FOV2)</strong></p> <p>Each image shows the same field of view (FOV), sequentially stained with the depicted fluorescence-labelled antibodies, including surface proteins, intracellular proteins and transcription factors. Images contain 2024 x 2024 pixels and are generated using an inverted wide-field fluorescence microscope with a 20x objective, a lateral resolution of 325 nm and an axial resolution above 5 µm. Images have been normalized and intensities adjusted.</p>
Multiplexed histology of COVID-19 post-mortem lung samples - CONROL CASE 3 FOV1
<p><strong>Image-based data set of a post-mortem lung sample from a COVID-19 donor (CONTROL CASE 3 FOV1)</strong></p> <p>Each image shows the same field of view (FOV), sequentially stained with the depicted fluorescence-labelled antibodies, including surface proteins, intracellular proteins and transcription factors. Images contain 2024 x 2024 pixels and are generated using an inverted wide-field fluorescence microscope with a 20x objective, a lateral resolution of 325 nm and an axial resolution above 5 µm. Images have been normalized and intensities adjusted.</p>
Multiplexed histology of COVID-19 post-mortem lung samples - PROLONGED CASE 2 FOV2
<p><strong>Image-based data set of a post-mortem lung sample from a COVID-19 donor (PROLONGED CASE 2 FOV2)</strong></p> <p>Each image shows the same field of view (FOV), sequentially stained with the depicted fluorescence-labelled antibodies, including surface proteins, intracellular proteins and transcription factors. Images contain 2024 x 2024 pixels and are generated using an inverted wide-field fluorescence microscope with a 20x objective, a lateral resolution of 325 nm and an axial resolution above 5 µm. Images have been normalized and intensities adjusted.</p>
Multiplexed histology of COVID-19 post-mortem lung samples - ACUTE CASE 1 FOV1
<p><strong>Image-based data set of a post-mortem lung sample from a COVID-19 donor (ACUTE CASE 1 FOV1)</strong></p> <p>Each image shows the same field of view (FOV), sequentially stained with the depicted fluorescence-labelled antibodies, including surface proteins, intracellular proteins and transcription factors. Images contain 2024 x 2024 pixels and are generated using an inverted wide-field fluorescence microscope with a 20x objective, a lateral resolution of 325 nm and an axial resolution above 5 µm. Images have been normalized and intensities adjusted.</p>
Multiplexed histology of COVID-19 post-mortem lung samples - PROLONGED CASE 4 FOV1
<p><strong>Image-based data set of a post-mortem lung sample from a COVID-19 donor (PROLONGED CASE 4 FOV1)</strong></p> <p>Each image shows the same field of view (FOV), sequentially stained with the depicted fluorescence-labelled antibodies, including surface proteins, intracellular proteins and transcription factors. Images contain 2024 x 2024 pixels and are generated using an inverted wide-field fluorescence microscope with a 20x objective, a lateral resolution of 325 nm and an axial resolution above 5 µm. Images have been normalized and intensities adjusted.</p>
Multiplexed histology of COVID-19 post-mortem lung samples - CONTROL CASE 1 FOV3
<p><strong>Image-based data set of a post-mortem lung sample from a non-COVID-related pneumonia donor (CONTROL CASE 1 FOV3)</strong></p> <p>Each image shows the same field of view (FOV), sequentially stained with the depicted fluorescence-labelled antibodies, including surface proteins, intracellular proteins and transcription factors. Images contain 2024 x 2024 pixels and are generated using an inverted wide-field fluorescence microscope with a 20x objective, a lateral resolution of 325 nm and an axial resolution above 5 µm. Images have been normalized and intensities adjusted.</p>
Multiplexed histology of COVID-19 post-mortem lung samples - CHRONIC CASE 1 FOV3
<p><strong>Image-based data set of a post-mortem lung sample from a COVID-19 donor (CHRONIC CASE 1 FOV3)</strong></p> <p>Each image shows the same field of view (FOV), sequentially stained with the depicted fluorescence-labelled antibodies, including surface proteins, intracellular proteins and transcription factors. Images contain 2024 x 2024 pixels and are generated using an inverted wide-field fluorescence microscope with a 20x objective, a lateral resolution of 325 nm and an axial resolution above 5 µm. Images have been normalized and intensities adjusted.</p>
Multiplexed histology of COVID-19 post-mortem lung samples - PROLONGED CASE 3 FOV1
<p><strong>Image-based data set of a post-mortem lung sample from a COVID-19 donor (PROLONGED CASE 3 FOV1)</strong></p> <p>Each image shows the same field of view (FOV), sequentially stained with the depicted fluorescence-labelled antibodies, including surface proteins, intracellular proteins and transcription factors. Images contain 2024 x 2024 pixels and are generated using an inverted wide-field fluorescence microscope with a 20x objective, a lateral resolution of 325 nm and an axial resolution above 5 µm. Images have been normalized and intensities adjusted.</p>
Multiplexed histology of COVID-19 post-mortem lung samples - PROLONGED CASE 2 FOV1
<p><strong>Image-based data set of a post-mortem lung sample from a COVID-19 donor (PROLONGED CASE 2 FOV1)</strong></p> <p>Each image shows the same field of view (FOV), sequentially stained with the depicted fluorescence-labelled antibodies, including surface proteins, intracellular proteins and transcription factors. Images contain 2024 x 2024 pixels and are generated using an inverted wide-field fluorescence microscope with a 20x objective, a lateral resolution of 325 nm and an axial resolution above 5 µm. Images have been normalized and intensities adjusted.</p>
Multiplexed histology of COVID-19 post-mortem lung samples - ACUTE CASE 1 FOV2
<p><strong>Image-based data set of a post-mortem lung sample from a COVID-19 donor (ACUTE CASE 1 FOV2)</strong></p> <p>Each image shows the same field of view (FOV), sequentially stained with the depicted fluorescence-labelled antibodies, including surface proteins, intracellular proteins and transcription factors. Images contain 2024 x 2024 pixels and are generated using an inverted wide-field fluorescence microscope with a 20x objective, a lateral resolution of 325 nm and an axial resolution above 5 µm. Images have been normalized and intensities adjusted.</p>
Multiplexed histology of COVID-19 post-mortem lung samples - CONROL CASE 2 FOV2
<p><strong>Image-based data set of a post-mortem lung sample from a COVID-19 donor (CONTROL CASE 2 FOV2)</strong></p> <p>Each image shows the same field of view (FOV), sequentially stained with the depicted fluorescence-labelled antibodies, including surface proteins, intracellular proteins and transcription factors. Images contain 2024 x 2024 pixels and are generated using an inverted wide-field fluorescence microscope with a 20x objective, a lateral resolution of 325 nm and an axial resolution above 5 µm. Images have been normalized and intensities adjusted.</p>
Multiplexed histology of COVID-19 post-mortem lung samples - PROLONGED CASE 3 FOV2
<p><strong>Image-based data set of a post-mortem lung sample from a COVID-19 donor (PROLONGED CASE 3 FOV2)</strong></p> <p>Each image shows the same field of view (FOV), sequentially stained with the depicted fluorescence-labelled antibodies, including surface proteins, intracellular proteins and transcription factors. Images contain 2024 x 2024 pixels and are generated using an inverted wide-field fluorescence microscope with a 20x objective, a lateral resolution of 325 nm and an axial resolution above 5 µm. Images have been normalized and intensities adjusted.</p>
Multiplexed histology of COVID-19 post-mortem lung samples - Single-cell Mean Fluorescence Intensities
<p>Data table containing single-cell mean fluorescence intensities (MFI) of all markers analyzed by multiplexed histology in all COVID-19 post-mortem lung samples and non-COVID-related pneumonia controls (14 lung samples, stratified based on disease duration into control, acute, chronic and prolonged). It contains information at the single-cell level about approx 50 proteins in around 40.000 lung cells.</p> <p>Data shown has been arcsin(h) transformed with a co-factor of 0.2. Additionally, cells expressing less than 0.15 MFI of all markers have been labeled as non-defined and excluded from the data set.</p> <p>Seurat package 4.0.0 was used in R to perform mean centering and scaling, followed by PCA, and reduced the dimensions of the data to the top 11 principal components. UMAP was initialized in this PCA space to visualize the data on reduced UMAP dimensions. The cells were clustered on PCA space using the SNN algorithm implemented as <em>FindNeighbors</em> and <em>FindClusters </em>with <em>n.epochs = 500</em> and default parameters (<em>res = 0.8</em>). We obtained 26 clusters that we merged to get relevant populations for our analysis based on canonical lineage markers. We ended up with 8 cell clusters that were manually annotated based on cell-type-specific markers found to be differentially expressed.</p> <p> </p> <p> </p>
Multiplexed histology of COVID-19 post-mortem lung samples - CHRONIC CASE 3 FOV1
<p><strong>Image-based data set of a post-mortem lung sample from a COVID-19 donor (CHRONIC CASE 3 FOV1)</strong></p> <p>Each image shows the same field of view (FOV), sequentially stained with the depicted fluorescence-labelled antibodies, including surface proteins, intracellular proteins and transcription factors. Images contain 2024 x 2024 pixels and are generated using an inverted wide-field fluorescence microscope with a 20x objective, a lateral resolution of 325 nm and an axial resolution above 5 µm. Images have been normalized and intensities adjusted.</p>
Multiplexed histology of COVID-19 post-mortem lung samples - CHRONIC CASE 3 FOV2
<p><strong>Image-based data set of a post-mortem lung sample from a COVID-19 donor (CHRONIC CASE 3 FOV2)</strong></p> <p>Each image shows the same field of view (FOV), sequentially stained with the depicted fluorescence-labelled antibodies, including surface proteins, intracellular proteins and transcription factors. Images contain 2024 x 2024 pixels and are generated using an inverted wide-field fluorescence microscope with a 20x objective, a lateral resolution of 325 nm and an axial resolution above 5 µm. Images have been normalized and intensities adjusted.</p>
A high-throughput 3D X-ray histology facility for biomedical research and preclinical applications - Underlying Data
<p><strong>Video files and logs</strong></p> <p>Single-slice and thick-slice roll* source videos are included. Each video is accompanied by a .txt log that contains information about the source file, slice thickness, and a brief description of the visualization mode.</p> <p>List of files:</p> <ul> <li>20211019-23h59m_20xAvgInt.mp4</li> <li>20211019-23h59m_20xAvgInt.txt</li> <li>20211019-23h59m_20xMaxInt.mp4</li> <li>20211019-23h59m_20xMaxInt.txt</li> <li>20211019-23h59m_20xStDev.mp4</li> <li>20211019-23h59m_20xStDev.txt</li> <li>20211019-23h59m_XYSliceRoll.mp4</li> <li>20211019-23h59m_XYSliceRoll.txt</li> <li>20211019-23h59m_XZSliceRoll.mp4</li> <li>20211019-23h59m_XZSliceRoll.txt</li> <li>20211019-23h59m_YZSliceRoll.mp4</li> <li>20211019-23h59m_YZSliceRoll.txt</li> </ul> <p>* <em>Thick-slice rolling is a 2D thick-slice viewing that allows rolling of a pre-selected number of slices (n) along the z-axis of the 3D data. A single thick-slice roll forwards is accomplished by translating the thick-slice by one single slice forwards; that is moving forward by one (+1) slice from the first and nth element and reapplying the criteria or operations to the new slice sub-stack.</em></p> <p><strong>Volume XRH data</strong><br> These are processed raw volume file saved in .raw and/or .tiff format, which are resliced to a histology-relevant orientation and/or have been enhanced using noise reduction (3D median filter) and/or ct-artefact removal techniques (e.g. cBC identifies a bandpass filter used to remove intensity variations originating from the histology cassette).</p> <p>List of volume files:</p> <ul> <li><strong>32220_20200703_XRH_2504_OLK_DEMO02019-FFPE_1620x1959x164x16bit.raw</strong> <ul> <li>sample: Human lung adenocarcinoma</li> <li>histology-relevant resliced volume (2x2x2 3D medial filter applied)</li> <li>import as 1620 x 1959 x 164 x 16-bit, big-endian; voxel edge size (mm): 0.0160042 isotropic</li> </ul> </li> <li><strong>cBC_32220_20200703_XRH_2504_OLK_DEMO02019-FFPE_1588x1674x164x16bit.raw</strong> <ul> <li>sample: Human lung adenocarcinoma</li> <li>cassette artefacts background correction (bandpass) of volume 32220_20200703_XRH_2504_OLK_DEMO02019-FFPE_1620x1959x164x16bit.raw</li> <li>import as 1620 x 1959 x 164 x 16-bit, big-endian; voxel edge size (mm): 0.0160042 isotropic</li> </ul> </li> <li><strong>Med3D_HPass_2111_20190606_MEDX_2234_EH_HN2_recon_2000x1952x501x32bit.raw</strong> <ul> <li>sample: Human head and neck tumour</li> <li>histology-relevant resliced volume (1x1x1 3D medial filter applied)</li> <li>import as 2000 x 1952 x 501 x 32-bit, big-endian; voxel edge size (mm): 0.00999782 isotropic</li> </ul> </li> </ul> <p><strong>Conventional Histology and correlative imaging</strong></p> <ul> <li><strong>HN2_Level001_MEDX080_Manual_BW_Series4.tif</strong> <ul> <li>H&E histology slice of the human head and neck tumour sample shown in "Med3D_HPass_2111_20190606_MEDX_2234_EH_HN2_recon_2000x1952x501x32bit.raw"</li> </ul> </li> <li><strong>HN2_Level001_MEDX080_Manual_BW</strong> <ul> <li>manual landmark selection used for registering the conventional histology slice onto the μCT slice</li> </ul> </li> <li><strong>HN2_MEDX_rotated_0080.tif</strong> <ul> <li>Slice 80 from volume "Med3D_HPass_2111_20190606_MEDX_2234_EH_HN2_recon_2000x1952x501x32bit.raw" that corresponds to histological slice "HN2_Level001_MEDX080_Manual_BW"</li> </ul> </li> </ul>
Fig. 4 in Kidney anatomy, histology and histometric traits associated to renosomatic index in Gymnotus inaequilabiatus (Gymnotiformes: Gymnotidae)
Fig. 4. Histological cross-sections of the head and exocrine kidney demonstrating different granulomatous structures in Gymnotus inaequilabiatus. a. severe aggregation of MMCs outer to granuloma in the exocrine kidney; PAS, bar scale = 20 µm. b. a clump of melanogenic macrophages (dark pigmented cells) adjacent to granuloma in the head kidney. The hematopoietic tissue is edematous and atypical. Some rodlet cells (black arrow) are observed. Granuloma presents a compact and thick layer of collagen with internal necrotic content surrounded by epithelioid cells (white arrows); H&E, bar scale = 10 µm. c. two well-defined granulomas with substantial internal necrotic content involved by fibrous tissue. A slight layer of MMCs aggregates close to the external wall of granuloma. TM, bar scale = 10 µm. d. MMCs aggregates both internally and externally to granuloma in the exocrine kidney. HE, bar scale = 10 µm.
Fig. 2 in Kidney anatomy, histology and histometric traits associated to renosomatic index in Gymnotus inaequilabiatus (Gymnotiformes: Gymnotidae)
Fig. 2. Cross-section of the head and exocrine kidney in Gymnotus inaequilabiatus. a. a transitional area between head (HE) and exocrine kidney (EX) drained by postcardinal vein (PCV). Lymphohematopoietic tissue is abundant in the head portion. MMCs are diffusely distributed in both portions. A thick fibrous capsule covers the organ (white arrow); HE, bar scale = 500 µm. b. the general aspect of the head kidney. Vascular sinusoids (white arrows) surrounding the lymphohematopoietic tissue enclosing the MMCs (black arrow); HE, bar scale = 200 µm. c. interstitial lymphohematopoietic tissue with MMCs deposits characterizes the exocrine kidney, in addition, the contoured tubules; renal corpuscle (white arrow); HE, bar scale = 200 µm. d. the exocrine kidney with a proximal convoluted tubule showing hyaline degeneration of the tubular epithelium often found in this species; HE, bar scale = 100 µm. e. exocrine kidney showing the corpuscle of Stannius (*). This structure is not lobulated, and is delimited by a fibrous capsule, and situated at the junction between head and exocrine portions; HE, bar scale = 500 µm. f. detail of junction between lymphohematopoietic tissue and corpuscle of Stannius in the head kidney. Fiber bundles subdivide both structures. Rodlet cells (white arrow), macrophages (M) and eosinophilic granulocytic cells (black arrow); granulocytic (G) and secretory cells (SC) internally fill the corpuscle; HE, bar scale = 50 µm.
Validation data set for automatic blood vessel segmentation in colorectal cancer histology (IHC)
<p><strong>Content</strong></p> <p>This data set contains 100 histological image patches of 1000 * 1000 px size. The samples were immunostained for CD34 (3,3'-Diaminobenzidine, DAB [brown]) with hematoxylin (blue) counterstain.</p> <p>Furthermore, the data set contains a table of blood vessel counts in each image by three blinded observers as well as an automatic count with a method based on the following paper:</p> <p>Kather, Jakob Nikolas et al. "Continuous Representation Of Tumor Microvessel Density And Detection Of Angiogenic Hotspots In Histological Whole-Slide Images". <em>Oncotarget</em> 6.22 (2015): 19163-19176. http://dx.doi.org/10.18632/oncotarget.4383</p> <p><strong>Image format</strong></p> <p>All images are RGB, 0.50 µm per pixel, digitized with an Aperio ScanScope (Aperio/Leica biosystems), magnification 20x. Histological samples are fully anonymized images of formalin-fixed paraffin-embedded human colorectal adenocarcinomas (primary tumors and liver metastases) from our pathology archive (Institute of Pathology, University Medical Center Mannheim, Heidelberg University, Mannheim, Germany).</p> <p><strong>Ethics statement</strong></p> <p>All experiments were approved by the institutional ethics board (medical ethics board II, University Medical Center Mannheim, Heidelberg University, Germany; approval 2015-868R-MA). The institutional ethics board waived the need for informed consent for this retrospective analysis of anonymized samples. All experiments were carried out in accordance with the Declaration of Helsinki.</p> <p><strong>Contact</strong></p> <p>For questions, please contact:<br> Dr. Jakob Nikolas Kather<br> http://orcid.org/0000-0002-3730-5348<br> ResearcherID: D-4279-2015</p>
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