Dataset Open Access
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
Karl Bellve;
Alessandro Rigano;
Kevin Fogarty;
Caterina Strambio-De-Castillia
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.
For this use case, which is presented in Figure 5 of Rigano et al., 2021, Micro-Meta App was utilized to document:
1) The Hardware Specifications 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 Tier 3 (Manufacturing/Technical Development/Full Documentation) as specified by the 4DN-BINA-OME Microscopy Metadata model (Hammer et al., 2021).
The TESM Hardware Specifications are stored in: Rigano et al._Figure 5_UseCase_Biomedical Imaging Group_TESM.JSON
2) The Image Acquisition Settings 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: Rigano et al._Figure 5_UseCase_AS_fswt-6hvirus-10minfix-stk_4-epi.tif.JSON
Instructional video tutorials on how to use these example data files:
Use these videos to get started with using Micro-Meta App after downloading the example data files available here.
| Name | Size | |
|---|---|---|
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FSWT-6hVirus-10minFIX-stk_4-EPI.tif.ome.tif
md5:e672e48ff807429f1b7b8adff97273c9 |
157.5 MB | Download |
|
rigano_et_al_2021_fswt-6hvirus-10minfix-stk_4-epi.tif_as.json
md5:21ce5f0fed889aea34bb9f358364c782 |
110.5 kB | Download |
|
rigano_et_al_2021_umms_big_olympus_ix71_tesm.json
md5:41b395ab938c28f0a217c7b594785282 |
103.3 kB | Download |
Rigano A, Ehmsen S, Ozturk SU, Ryan J, Balashov A, Hammer M, et al. Micro-Meta App: an interactive software tool to facilitate the collection of microscopy metadata based on community-driven specifications. BioRxiv [Internet]. 2021; Available from: https://www.biorxiv.org/content/10.1101/2021.05.31.446382v1
Hammer M, Huisman M, Rigano A, Boehm U, Chambers JJ, Gaudreault N, et al. Towards community-driven metadata standards for light microscopy: tiered specifications extending the OME model. BioRxiv [Internet]. 2021 Apr 25; Available from: https://www.biorxiv.org/content/10.1101/2021.04.25.441198v1
Huisman M, Hammer M, Rigano A, Boehm U, Chambers JJ, Gaudreault N, et al. A perspective on Microscopy Metadata: data provenance and quality control [Internet]. arXiv [q-bio.QM]. 2021. Available from: https://arxiv.org/abs/1910.11370
1/2 Instructional video on how to use these example data files to get started with Micro-Meta App. Available at: 1/2 Instructional video on how to use these example data files to get started with Micro-Meta App. Available at: https://vimeo.com/562022222
1/2 Instructional video on how to use these example data files to get started with Micro-Meta App. Available at: 1/2 Instructional video on how to use these example data files to get started with Micro-Meta App. Available at: https://vimeo.com/562022281
Hammer, M., Huisman, M., Rigano, A. et al. Towards community-driven metadata standards for light microscopy: tiered specifications extending the OME model. Nat Methods 18, 1427–1440 (2021). https://doi.org/10.1038/s41592-021-01327-9
Rigano, A., Ehmsen, S., Öztürk, S.U. et al. Micro-Meta App: an interactive tool for collecting microscopy metadata based on community specifications. Nat Methods 18, 1489–1495 (2021). https://doi.org/10.1038/s41592-021-01315-z
| All versions | This version | |
|---|---|---|
| Views | 543 | 285 |
| Downloads | 207 | 42 |
| Data volume | 10.4 GB | 2.4 GB |
| Unique views | 429 | 209 |
| Unique downloads | 100 | 15 |
- Publication date:
- January 19, 2022
- DOI:
-
- Keyword(s):
- Microscopy Metadata Imaging Reproducibility Quality Control Data Provenance Data Sharing
- Grants:
-
National Institutes of Health:
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4D Nucleome Network Data Coordination and Integration Center (5U01CA200059-03)
- Visualizing local and global chromatin architecture, and gene expression in the individual cell by structural (SUSHI) and temporal (3D-SMRT) single molecule imaging (1U01EB021238-01)
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4D Nucleome Network Data Coordination and Integration Center (5U01CA200059-03)
- License (for files):
- Creative Commons Attribution 4.0 International