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11 results for “epifluorescence”
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>
Cell counts (per liter) by size groups of diatoms, autotrophic and heterotrophic plankton, via epifluorescent microscopy (EPI) from CCE LTER process cruises in the California Current region, 2006 - 2016.
Microbial community assemblages of the California Current Ecosystem (CCE) are assessed for abundance of diatoms, autotrophic (dinoflagellate and other eukaryotes) and heterotrophic (dinoflagellate and other eukaryotes) plankton using high-throughput digital epifluorescence microscopy (EPI). Samples to estimate the nano- and microplankton (0.2-2.0-µm and 2.0-20-µm size, respectively) are collected at various depths, preserved, stained, and filtered onto a membrane filter and mounted on a glass microscope slide aboard the process cruises (since 2006, ongoing). Slides are then frozen at -80°C for subsequent imaging and analysis in the laboratory onshore.
Size group (pico, nano, micro) and group total carbon estimates from cell counts via epifluorescent microscopy (EPI) of heterotrophic and autotrophic plankton from CCE LTER process cruises in the California Current region, 2006 - 2016
Microbial community assemblages of the California Current Ecosystem (CCE) are assessed for biomass of heterotrophic (dinoflagellate and other eukaryotes) and autotrophic (dinoflagellate and other eukaryotes) plankton using high-throughput digital epifluorescence microscopy (EPI). Samples to estimate the nano- and microplankton (0.2-2.0-µm and 2.0-20-µm size, respectively) are collected at various depths, preserved, stained, and filtered onto a membrane filter and mounted on a glass microscope slide aboard the process cruises (since 2006, ongoing). Slides are then frozen at -80°C for subsequent imaging and analysis in the laboratory onshore. Carbon biomass is computed from cell biovolumes.
Size group (pico, nano, micro) and group total carbon estimates from cell counts via epifluorescent microscopy (EPI) of heterotrophic and autotrophic plankton from CCE-CalCOFI Augmented cruises in the California Current System, 2004 - 2011 (ongoing).
Microbial community assemblages of the California Current Ecosystem (CCE) are assessed for biomass of heterotrophic (dinoflagellate and other eukaryotes) and autotrophic (dinoflagellate and other eukaryotes) plankton using high-throughput digital epifluorescence microscopy (EPI). Samples to estimate the nano- and microplankton (0.2-2.0-µm and 2.0-20-µm size, respectively) are collected at various depths via Niskin bottles, preserved, stained, and filtered onto a membrane filter and mounted on a glass microscope slide aboard the quarterly CalCOFI survey cruises (since 2004, ongoing). Slides are then frozen at -80°C for subsequent imaging and analysis in the laboratory onshore. Carbon biomass is computed from cell biovolumes.
Cell counts (per liter) by size groups of diatoms, autotrophic and heterotrophic plankton, via epifluorescent microscopy (EPI) from CCE-CalCOFI Augmented cruises in the California Current System, 2004 - 2011 (ongoing).
Microbial community assemblages of the California Current Ecosystem (CCE) are assessed for abundance of diatoms, autotrophic (dinoflagellate and other eukaryotes) and heterotrophic (dinoflagellate and other eukaryotes) plankton using high-throughput digital epifluorescence microscopy (EPI). Samples to estimate the nano- and microplankton (0.2-2.0-µm and 2.0-20-µm size, respectively) are collected at various depths via Niskin bottles, preserved, stained, and filtered onto a membrane filter and mounted on a glass microscope slide aboard the quarterly CalCOFI survey cruises (since 2004, ongoing). Slides are then frozen at -80°C for subsequent imaging and analysis in the laboratory onshore.
Nano- and Microplastic Abundance, analyzed with Epifluorescence microscopy, collected aboard two student cruises on two student cruises, SKrillEx I (July 2014) and SKrillEx II (June 2015).
Surface seawater was collected in stainless steel buckets in the nearshore California Current on two student cruises, SKrillEx I (July 2014) and SKrillEx II (June 2015). Surface seawater samples were filtered on to 5-µm pore polycarbonate filters, and frozen at sea for later analysis. Once back on land, the frozen transparent polycarbonate (PC) filters were filtered on an all-glass apparatus and then imaged with modified epifluorescence microscopy techniques for microplastic particles. All microplastic particles were analyzed for plastic shape, length, surface area, and fluorescence.
Nano- and Microplastic Particle Lengths and Surface Areas, analyzed with Epifluorescence microscopy, collected aboard two student cruises, SKrillEx I (July 2014) and SKrillEx II (June 2015).
Surface seawater was collected in stainless steel buckets aboard two student cruises, SKrillEx I (July 2014) and SKrillEx II (June 2015). Surface seawater samples were filtered on to 5-µm pore polycarbonate filters, and frozen at sea for later analysis. Once back on land, the frozen transparent polycarbonate (PC) filters were filtered on an all-glass apparatus and then imaged with modified epifluorescence microscopy techniques for microplastic particles. All microplastic particles were analyzed for plastic shape, length, surface area, and fluorescence.
Salp ingestion rates of microplastics, analyzed with Epifluorescence microscopy, collected aboard multiple cruises (SEAPLEX, SKrillEx I, and SKrillEx II)
Salps were collected on SKrillEx I and II during nightly transects in 202-μm mesh bongo tows, towed to approximately 200 m depth, and samples were preserved in 5% formaldehyde buffered with sodium tetraborate. We also used zooplankton samples collected on the August 2009 SEAPLEX cruise, where samples were collected using a manta net, 333-μm mesh, towed for 15 minutes at the surface, with samples preserved in 5% formaldehyde buffered with sodium tetraborate. Salps were identified to species, life history phase (oozooid or blastozooid), and measured for zooid length. The length of the stomach was measured, noted for degree of fullness, and dissected from each salp. Dissected salp stomachs were cut in half and placed in 15 mL of Milli-Q water for at least 24 hours to soften and release gut contents. The contents were then vacuum-filtered onto 5-μm pore polycarbonate filters with an additional 70 mL of Milli-Q water to aid in filtration. Those filters were analyzed with modified epifluoresecence microscopy techniques for microplastic particles. All microplastic particles were analyzed for plastic shape, length, surface area, and fluorescence. Ingestion rate of particles/hour for each salp was measured.
Ingested Nano- and Microplastic Particle Lengths and Surface Areas, dissected from salp guts, analyzed with Epifluorescence microscopy, collected aboard multiple cruises SEAPLEX in 2009, SKrillEx I in 2014, and SKrillEx II in 2015.
Salps were collected on SKrillEx I and II during nightly transects in 202-μm mesh bongo tows, towed to approximately 200 m depth, and samples were preserved in 5% formaldehyde buffered with sodium tetraborate. We also used zooplankton samples collected on the August 2009 SEAPLEX cruise, where samples were collected using a manta net, 333-μm mesh, towed for 15 minutes at the surface, with samples preserved in 5% formaldehyde buffered with sodium tetraborate. Salps were identified to species, life history phase (oozooid or blastozooid), and measured for zooid length. The length of the stomach was measured, noted for degree of fullness, and dissected from each salp. Dissected salp stomachs were cut in half and placed in 15 mL of Milli-Q water for at least 24 hours to soften and release gut contents. The contents were then vacuum-filtered onto 5-μm pore polycarbonate filters with an additional 70 mL of Milli-Q water to aid in filtration. Those filters were analyzed with modified epifluoresecence microscopy techniques for microplastic particles. All microplastic particles were analyzed for plastic shape, length, surface area, and fluorescence.
Nano- and Microplastic Particle Lengths and Surface Areas, analyzed with Epifluorescence microscopy, collected aboard the student cruise on R/V Falkor (2013).
Surface seawater was collected in stainless steel buckets on a transect from Seattle to Honolulu, in October 2013. Surface seawater samples were filtered on to 5-µm pore polycarbonate filters, and frozen at sea for later analysis. Once back on land, the frozen transparent polycarbonate (PC) filters were filtered on an all-glass apparatus and then imaged with modified epifluorescence microscopy techniques for microplastic particles. All microplastic particles were analyzed for plastic shape, length, surface area, and fluorescence.
Nano- and Microplastic Abundance, analyzed with Epifluorescence microscopy, collected aboard the student cruise on R/V Falkor (2013).
Surface seawater was collected in stainless steel buckets on a transect from Seattle to Honolulu, in October 2013. Surface seawater samples were filtered on to 5-µm pore polycarbonate filters, and frozen at sea for later analysis. Once back on land, the frozen transparent polycarbonate (PC) filters were filtered on an all-glass apparatus and then imaged with modified epifluorescence microscopy techniques for microplastic particles. All microplastic particles were analyzed for plastic shape, length, surface area, and fluorescence.
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OpenNeuro
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