Whole slide images of different specimens from the Smithsonian Natural History Collection - Part IV
Authors/Creators
- 1. Smithsonian National Museum of Natural History Department of Paleobiology
- 2. USDA APHIS PPQ
-
3.
Smithsonian Institution
Description
This folder contains three NanoZoomer Digital Pathology Images (NDPI) from whole-scanned slides containing three insects, including small white flies and beetles. It also contains an excel file with the information about the specimens imaged.
To open, managing and analyze these NDPI files, Hamamatsu created NDP.view2, a free software (Hamamatsu 2018). There are also other free and open-access software tools created to open not only NDPI files but other propertary whole-slide images (WSI), such as: a) ImageJ Fiji, which has the NDPITools ImageJ plugin to convert the slides to standard TIFF format (Schindelin et al. 2012); and b) OpenSlide, a C library that provides a simple interface for reading the images (Goode et al. 2013). This can be used through different interfaces or platforms, such as Python with OpenSlide-Python, through OMERO (Open Microscopy Environment), and QuPath (Open Software for Bioimage Analysis).
Files
Files
(6.7 GB)
| Name | Size | Download all |
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md5:5fd95120a02241551277cd945afd42cb
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2.3 GB | Download |
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md5:b6336d2a0b81cf92aa8e94dea2d390e1
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1.3 GB | Download |
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md5:2f481941ec759458d071c492a64bf169
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3.2 GB | Download |
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md5:0e62c3566f43b14fe0436919a23e7a00
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13.5 kB | Download |
Additional details
Related works
- Is supplement to
- Journal article: 10.1371/journal.pone.0346139 (DOI)
Funding
- Smithsonian Institution
- Life on a Sustainable Planet Pathfinder Grant: Effects of extreme global warming on the distribution of terrestrial plants
- Smithsonian Institution
- Smithsonian Climate Change Fellowship: Our Shared Future: Life on a Sustainable Planet
- National Museum of Natural History
- Office of the Associated Director for Science
- Smithsonian Institution
- Office of the Undersecretary for Science
- Smithsonian Institution
- The Bill and Dianne Ryan Family
References
- Hamamatsu. NDP.view2 Image viewing software [Internet]. 2018 [cited 2024 Apr 6]. Available from: https://www.hamamatsu.com/jp/en/product/life-science-and-medical-systems/digital-slide-scanner/U12388-01.html
- Schindelin J, Arganda-Carreras I, Frise E. Fiji: an open-source platform for biological-image analysis. Nat Methods. 2012;9:676–82
- Goode A, Gilbert B, Harkes J, Jukic D, Mahadev SM. OpenSlide: A vendor-neutral software foundation for digital pathology. J Pathol Inform. 2013;4(1):2153–3539