Whole slide images of different specimens from the Smithsonian Natural History Collection - Part I
Authors/Creators
- 1. Smithsonian National Museum of Natural History Department of Paleobiology
-
2.
Smithsonian Institution
- 3. Smithsonian Tropical Research Institute
Description
This compressed ZIP folder contains two NanoZoomer Digital Pathology Images (NDPI) from two whole-scanned slides and one NDPA file (NDP annotation), which is an XML-based format file. One of the NDPI images contains fossil pollen specimens. This file is accompained by the NDPA file and contains annotations for the fossil pollen material. These annotations include regions of interest and labels. The second NDPI file contains modern diatoms.
To access these files the folder needs to be uncompressed first. Then, to open, manage, 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 information
| File | 1 | 2 |
| File name | 1_D8401-A_L_2024_01_18_13_05_54_Alaska.ndpi | 2_2703_USGS_2023-11-06 10_16_13.ndpi |
| 1_D8401-A_L_2024_01_18_13_05_54_Alaska.ndpi.npda | -- | |
| Specimen | Fossil pollen | Diatoms |
| Specimen ID | D8401 | 3534 |
| Locality | Fort Yukon | Virgin Valley |
| State | Alaska | Nevada |
| Country | USA | USA |
| Museum | Smithsonian NMNH | Smithsonian NMNH |
| Collection | Paleobotany | Botany |
| Collector/Analyst | T. A. Ager | K. E. Lohman |
| Area scanned (mm) | 20.2 x 20.6 | 19.3 x 20 |
| Z-Stack | 25 | 15 |
| Interval between Layers (um) | 1 | 1 |
| Focus range (um) | -12 to 12 | -7 to 7 |
| Scanning Time | 18 m 37 s | 10 m 24 s |
| File Size (GB) | 27.9 | 19 |
Files
Dataset_1.zip
Files
(50.0 GB)
| Name | Size | Download all |
|---|---|---|
|
md5:01cd2e837c37268fe006a3e6239f4b85
|
50.0 GB | Preview 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