DOI: 10.5281/zenodo.4891882
title: 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

description: <strong>Example Microscopy Metadata JSON files produced using the Micro-Meta App documenting an example raw-image file acquired using the custom-built TIRF Epifluorescence Structured Illumination Microscope.</strong> For this use case, which is presented in Figure 5 of Rigano et al., 2021, Micro-Meta App was utilized to document: 1) The <strong>Hardware Specifications</strong> of the custom build TIRF Epifluorescence Structured light Microscope (TESM; Navaroli et al., 2010) 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 4DN-BINA-OME Microscopy Metadata model (Hammer et al., 2021). The TESM Hardware Specifications are stored in: <strong>Rigano et al._Figure 5_UseCase_Biomedical Imaging Group_TESM.JSON</strong> 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. 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> <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. Part 1/2 Part 2/2
description: Additional support: -- NSF grant #1917206 to D.G.; -- Chan Zuckerberg Initiative DAF (Silicon Valley Community Foundation) grant #2019-198155 (5022) awarded to C.S.D.C. as part of the Imaging Scientist Program. -- Chan Zuckerberg Initiative DAF (Silicon Valley Community Foundation) grant ##2020-225398 awarded to C.M.B. as part of the Imaging Scientist Program
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