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226 results for “Microscope image”
Example Microscopy Metadata JSON files produced using Micro-Meta App to document the acquisition of example images using a custom-built TIRF Epifluorescence Structured Illumination Microscope
<p><strong>Example Microscopy Metadata JSON files produced using the <a href="https://wu-bimac.github.io/MicroMetaApp.github.io/">Micro-Meta App</a> documenting an example raw-image file acquired using the custom-built TIRF Epifluorescence Structured Illumination Microscope.</strong></p> <p>For this use case, which is presented in Figure 5 of <a href="http://doi: https://doi.org/10.1101/2021.05.31.446382">Rigano et al., 2021</a>, Micro-Meta App was utilized to document:</p> <p>1) The <strong>Hardware Specifications</strong> of the custom build TIRF Epifluorescence Structured light Microscope (TESM; <a href="https://www.pnas.org/content/109/8/E471.long">Navaroli et al., 2010</a>) developed, built on the basis of the based on Olympus IX71 microscope stand, and owned by the Biomedical Imaging Group (http://big.umassmed.edu/) at the Program in Molecular Medicine of the University of Massachusetts Medical School. Because TESM was custom-built the most appropriate documentation level is <strong>Tier 3</strong> (<em>Manufacturing/Technical Development/Full Documentation</em>) as specified by the <a href="https://doi.org/10.5281/zenodo.4710731">4DN-BINA-OME</a> Microscopy Metadata model (<a href="https://doi.org/10.1101/2021.04.25.441198">Hammer et al., 2021</a>).</p> <p>The TESM Hardware Specifications are stored in: <strong>Rigano et al._Figure 5_UseCase_Biomedical Imaging Group_TESM.JSON</strong></p> <p>2) The <strong>Image Acquisition Settings</strong> that were applied to the TESM microscope for the acquisition of an example image (FSWT-6hVirus-10minFIX-stk_4-EPI.tif.ome.tif) obtained by Nicholas Vecchietti and Caterina Strambio-De-Castillia. For this image, TZM-bl human cells were infected with HIV-1 retroviral three-part vector (FSWT+PAX2+pMD2.G). Six hours post-infection cells were fixed for 10 min with 1% formaldehyde in PBS, and permeabilized. Cells were stained with mouse anti-p24 primary antibody followed by DyLight488-anti-Mouse secondary antibody, to detect HIV-1 viral Capsid. In addition, cells were counterstained using rabbit anti-Lamin B1 primary antibody followed by DyLight649-anti-Rabbit secondary antibody, to visualize the nuclear envelope and with DAPI to visualize the nuclear chromosomal DNA.</p> <p>The Image Acquisition Settings used to acquire the FSWT-6hVirus-10minFIX-stk_4-EPI.tif.ome.tif image are stored in: <strong>Rigano et al._Figure 5_UseCase_AS_fswt-6hvirus-10minfix-stk_4-epi.tif.JSON</strong></p> <p><em><strong>Instructional video tutorials on how to use these example data files:</strong></em><br> Use these videos to get started with using Micro-Meta App after downloading the example data files available here.</p> <ul> <li><a href="https://vimeo.com/562022222">Part 1/2</a></li> <li><a href="https://vimeo.com/562022281">Part 2/2</a></li> </ul>
Videos of the processed microscope images and time series of the petrophysical parameters from image processing and geochemical simulation and of the measured induced polarisation [Video][Dataset]
<p>Supporting Information for the manuscript <em>Microfluidics and spectral induced polarization for direct observation and petrophysical modeling of calcite dissolution</em> published in Geophysical Research Letters</p> <ul> <li><strong>Data Set S1.</strong> Porosity, water saturation, and calcite sample perimeter from image<br>processing.</li> <li><strong>Data Set S2.</strong> Porosity, water conductivity, and pH from geochemical simulation.</li> <li><strong>Data Set S3.</strong> Real and imaginary components of the complex electrical conductivity at<br>2.5 Hz and CEC from petrophysical modeling.</li> <li><strong>Movie S1.</strong> Dissolution of the calcite sample with the detected contour superimposed in<br>white on the grayscale images. Time, length scale, and flow direction are indicated. In<br>case of problems launching the file, we recommend using VLC Media Player software.</li> <li><strong>Movie S2.</strong> Segmented images of the CO2 bubbles produced by the calcite dissolution.<br>Time, length scale, and flow direction are indicated. In case of problems launching the<br>file, we recommend using VLC Media Player software.</li> </ul>
Scanning electron microscope images of spruce needle homogenate and scanning electron microscope images of isolated small cellular particles from spruce needle homogenate
<p>Scanning electron microscope images of spruce needle homogenate and of isolated small cellular particles from spruce needle homogenate are presented. Each image is supplemented by description of the preparation of the sample and the data on the imaging technique and equipment. The data are curated by Veronika Kralj-Iglic and University of Ljubljana, Faculty of Health Sciences, Laboratory of Clinical Biophysics, and Anna Romolo, presently at University of Ljubljana, Faculty of Electrical Engineering, Laboratory of Physics, Ljubljana, Slovenia. Present address of Marko Jeran is: Department of Inorganic Chemistry and Technology, “Jožef Stefan” Institute, Ljubljana, Slovenia.</p>
IODP Expedition 383 Scanning electron microscope images
Microscopic images of discrete samples were acquired using a scanning electron microscope (SEM) and captured as image files. These files were uploaded along with a brief description and a record of the microscopic conditions when the image was taken.
IODP Expedition 378 Scanning electron microscope images
<p>Microscopic images of discrete samples were acquired using a scanning electron microscope (SEM) and captured as image files. These files were uploaded along with a brief description and a record of the microscopic conditions when the image was taken.</p>
Using the traditional microscope for mineral grain orientation determination: A prototype image analysis pipeline for optic-axis mapping (POAM). Original dataset.
<p>The data repository contains data obtained with the microscope Nikon Eclipse LV100ND that was stitched with <a href="https://imagej.net/plugins/trakem2/">TrakEM2 software</a>. The files allow reproducing the results obtained and plot in <a href="https://doi.org/10.1111/jmi.13284">Acevedo et al. (2024)</a> <strong>"Using the traditional microscope for mineral grain orientation determination: A prototype image analysis pipeline for optic-axis mapping (POAM)."</strong> by Acevedo Zamora, M. A., Schrank, C. E., & Kamber, B. S.</p> <p>The prototype uses MatLab scripts (<a href="https://github.com/marcoaaz/AcevedoEtAl._2024a_POAM">AcevedoEtAl._2024a_POAM</a>) that were documented in the paper Supplementary Material 1. The metadata can be found in Supplementary Material 3 and follows the structure of this data repository. The user needs downloading and changing the paths to run the same scripts and reproduce the results.</p> <p>Note: After download, unzip and merge (copy-paste) the folders (parts 1, 2 and 3). Before merging, the containing folder should be re-named to 'paper 2_datasets' to match exactly the MatLab scripts and reproduce our work.</p> <p>The remaining questions should be addressed to Marco Acevedo (maaz.geologia@gmail.com ; marco.acevedozamora@qut.edu.au)</p> <p>Thanks.</p>
IODP Expedition 367 Scanning electron microscope images
Microscopic images of discrete samples were acquired using a scanning electron microscope (SEM) and captured as image files. These files were uploaded along with a brief description and a record of the microscopic conditions when the image was taken.
IODP Expedition 379 Scanning electron microscope images
Microscopic images of discrete samples were acquired using a scanning electron microscope (SEM) and captured as image files. These files were uploaded along with a brief description and a record of the microscopic conditions when the image was taken.
IODP Expedition 360 Scanning electron microscope images
Microscopic images of discrete samples were acquired using a scanning electron microscope (SEM) and captured as image files. These files were uploaded along with a brief description and a record of the microscopic conditions when the image was taken.
IODP Expedition 397 Scanning electron microscope images
Microscopic images of discrete samples were acquired using a scanning electron microscope (SEM) and captured as image files. These files were uploaded along with a brief description and a record of the microscopic conditions when the image was taken.
IODP Expedition 398 Scanning electron microscope images
Microscopic images of discrete samples were acquired using a scanning electron microscope (SEM) and captured as image files. These files were uploaded along with a brief description and a record of the microscopic conditions when the image was taken.
IODP Expedition 356 Scanning electron microscope images
Microscopic images of discrete samples were acquired using a scanning electron microscope (SEM) and captured as image files. These files were uploaded along with a brief description and a record of the microscopic conditions when the image was taken.
IODP Expedition 359 Scanning electron microscope images
Microscopic images of discrete samples were acquired using a scanning electron microscope (SEM) and captured as image files. These files were uploaded along with a brief description and a record of the microscopic conditions when the image was taken.
Diagnostic electron microscopy of viruses with low-voltage electron microscopes. Raw image files with brief description.
<p>The zipped data container contains the raw (unprocessed) images that we have used for the preparation of our manuscript entiteled:</p> <p>"Diagnostic electron microscopy of viruses with low-voltage electron microscopes" <a href="https://doi.org/10.1369%2F0022155420929438">https://doi.org/10.1369/0022155420929438</a></p> <p>Lars Möller, Gudrun Holland, Michael Laue</p> <p>Advanced Light and Electron Microscopy (ZBS 4), Centre for Biological Threats and Special Pathogens, Robert Koch Institute, D-13353 Berlin, Germany</p> <p>The brief description of the data set comprises the abstract of the manuscript, the figures (including captions) and a description of the materials and methods used for their generation.</p>
Microscope images of human cancer cell lines (U2OS and HL-60)
<p>This is a dataset that contains microscope images from two cell lines, namely, a human osteosarcoma cell line (U2OS) and a human leukemia cell line (HL-60). The dataset was originally prepared for the cell counting task. It contains 165 labeled images (training: 133, test: 32).</p> <p>The file contains three folders:</p> <p>- training: 165 labeled images in .tiff format;<br> - test: 32 labeled images in .tiff format.</p> <p>Each labeled image has the following name: X.Y.N.tiff</p> <p>where:<br> X - the name of the human cancer cell line;<br> Y - a condition identifier (irrelevant);<br> N - the cell count.</p> <p><br> If you use this dataset, please cite the following paper:</p> <ul> <li>Lavitt F, Rijlaarsdam DJ, van der Linden D, Weglarz-Tomczak E, Tomczak JM. Deep Learning and Transfer Learning for Automatic Cell Counting in Microscope Images of Human Cancer Cell Lines. <em>Applied Sciences</em>. 2021; 11(11):4912. https://doi.org/10.3390/app11114912</li> </ul>
IODP Expedition 366 Scanning electron microscope images
<p>Microscopic images of discrete samples were acquired using a scanning electron microscope (SEM) and captured as image files. These files were uploaded along with a brief description and a record of the microscopic conditions when the image was taken.</p>
Dataset accompanying manuscript "Correlative imaging of spatio-angular dynamics of biological systems with multimodal instant polarization microscope"
<p>Raw images and microscope calibration metadata for reconstruction of datasets presented in Fig. 1 and Fig. 3 of "Correlative imaging of spatio-angular dynamics of biological systems with multimodal instant polarization microscope". Notebooks demonstrating steps in the label-free and fluorescence anisotropy reconstruction pipelines can be found at https://github.com/mehta-lab/miPolScope.</p>
Scanning electron microscope images of Dunaliela tertiolecta and Phaeodactylum tricornutum cultures and scanning electron microscope images and cryogenic electron microscope images of isolated small cellular particles from respective conditioned media
<p>Scanning electron microscope images of cultures of microalgae<em> Dunaliela</em><em> </em><em>tertiolecta</em><em> </em>and <em>Phaeodactylum</em><em> </em><em>tricornutum</em><em> </em>and scanning electron microscope images and cryogenic electron microscope images of isolated small cellular particles from respective conditioned media are presented. Each image is supplemented by description of the preparation of the sample and the data on the imaging technique and equipment. The data are curated by Veronika Kralj-Iglic and Anna Romolo, University of Ljubljana, Faculty of Health Sciences, Laboratory of Clinical Biophysics.</p> <p> </p> <p> </p>
IODP Expedition 352 Scanning electron microscope images
<p>Microscopic images of discrete samples were acquired using a scanning electron microscope (SEM) and captured as image files. These files were uploaded along with a brief description and a record of the microscopic conditions when the image was taken.</p>
РИС. 8. Примеры проблем с иЗображением при работе на СЭМ. А, В. Засветка раЗличных частей раковин глохидиев (А. Anodonta anatina (=Colletopterum), оЗ. Красное, ХакасиЯ. В. Inversiunio reinianus, оЗ. Бива, о-в Хонсю, ЯпониЯ). C. РаЗнаЯ скорость сканированиЯ (слева – очень быстраЯ, справа – медленнаЯ) наружной поверхности глохидиЯ (Anodonta cygnea, р. Ялма, МосковскаЯ обл.). D. Артефакты в виде гориЗонтальных полос вследствие накоплениЯ отрицательного ЗарЯда при недостаточном напылении внутренней поверхности глохидиЯ (Nodularia douglasiae, ПетровскаЯ протока, бассейн р. Амур, Хабаровский кр.). МасШтаб 50 мкм (А, В), 2 мкм (С), 5 мкм (D). Микроскопы Zeiss EVO 40 (А, С, D), Zeiss MERLIN (В), напыление углеродом (А, С), хромом (В, D). FIG. 8. Illustration of different problems with SEM images. A, B. Overall illumination of some glochidia shells parts (A. Anodonta anatina (= Colletopterum), Krasnoe Lake, Khakassia. B. Inversiunio reinianus, Biwa Lake, Honshu Island, Japan). C. Different scanning speed (faster on the left and slower on the right) of the exterior glochidia valve (Anodonta cygnea, Yalma River, Moscow Oblast). D. Artifacts as horizontal stripes because of additional accumulation of a negative charge due to insufficient coating of the interior glochidia valve (Nodularia douglasiae, Petrovskaya channel, Amur River basin, Khabarovsk Krai). Scale bars 50 μm (A, B), 2 μm (C), 5 μm (D). Zeiss EVO 40 (A, C, D) and Zeiss MERLIN (B) microscopes, sputter coating with carbon (A, C) and chromium (B, D). in Методика подготовки раковин глохидиев (Bivalvia, Unionidae) длЯ работы на сканируюЩем Электронном микроскопе
РИС. 8. Примеры проблем с иЗображением при работе на СЭМ. А, В. Засветка раЗличных частей раковин глохидиев (А. Anodonta anatina (=Colletopterum), оЗ. Красное, ХакасиЯ. В. Inversiunio reinianus, оЗ. Бива, о-в Хонсю, ЯпониЯ). C. РаЗнаЯ скорость сканированиЯ (слева – очень быстраЯ, справа – медленнаЯ) наружной поверхности глохидиЯ (Anodonta cygnea, р. Ялма, МосковскаЯ обл.). D. Артефакты в виде гориЗонтальных полос вследствие накоплениЯ отрицательного ЗарЯда при недостаточном напылении внутренней поверхности глохидиЯ (Nodularia douglasiae, ПетровскаЯ протока, бассейн р. Амур, Хабаровский кр.). МасШтаб 50 мкм (А, В), 2 мкм (С), 5 мкм (D). Микроскопы Zeiss EVO 40 (А, С, D), Zeiss MERLIN (В), напыление углеродом (А, С), хромом (В, D). FIG. 8. Illustration of different problems with SEM images. A, B. Overall illumination of some glochidia shells parts (A. Anodonta anatina (= Colletopterum), Krasnoe Lake, Khakassia. B. Inversiunio reinianus, Biwa Lake, Honshu Island, Japan). C. Different scanning speed (faster on the left and slower on the right) of the exterior glochidia valve (Anodonta cygnea, Yalma River, Moscow Oblast). D. Artifacts as horizontal stripes because of additional accumulation of a negative charge due to insufficient coating of the interior glochidia valve (Nodularia douglasiae, Petrovskaya channel, Amur River basin, Khabarovsk Krai). Scale bars 50 μm (A, B), 2 μm (C), 5 μm (D). Zeiss EVO 40 (A, C, D) and Zeiss MERLIN (B) microscopes, sputter coating with carbon (A, C) and chromium (B, D).
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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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.