Title: Slide scan example for Automorph

Type Image Hsiang, Allison Y., Nealson, Kaylea, Elder, Leanne E., Sibert, Elizabeth C., Kahanamoku, Sara S., Burke, Janet E., Kelly, Abigail, Liu, Yusu, Hull, Pincelli M. (2016): Slide scan example for Automorph. Zenodo. Image. https://zenodo.org/record/167557

Authors: Hsiang, Allison Y. (Yale University) ; Nealson, Kaylea (Yale University) ; Elder, Leanne E. (Yale University) ; Sibert, Elizabeth C. (Harvard University) ; Kahanamoku, Sara S. (University of California, Berk) ; Burke, Janet E. (Yale University) ; Kelly, Abigail (Smithsonian Tropical Research Institute) ; Liu, Yusu (MIT) ; Hull, Pincelli M. (Yale University) ;

Links

• Item record in Zenodo
• Digital object URL

Summary

This dataset is an example of the slide scans of microfossils and Automorph output generated in P.M. Hull's lab at Yale University. The raw slide scan is contained in the file 'IP.307626_slide_scan.zip'; each tif is a z-slice of the entire imaged microfossil slide.  Note that the raw slide scan images are BigTIFFs, a file format that cannot be view in most commonly used programs.

Objects are segmented out and refocused (for image quality) in the Automorph routines 'segment' and 'focus'.  The 2D image output of these routines is contained in the file 'IP.307626_EDFs.zip' .  2D outlines and shape measurements are contained in the files 'IP.307626_2D_coordinates.csv' and 'IP.307626_2D_properties.csv', and were generated with the Automorph routine 'run2dmorph'.   3D pdfs of individual objects  are provided in 'IP.307626_3D_PDFs.zip' and were generated in the Automorph routine 'run3dmorph'.   3D meshes and measurements are also provided by 'run3dmorph' but are not included in this example dataset.  Note that only some pdf viewers are able to display 3D pdfs properly.

Automorph software and tutorials can be accessed here: https://github.com/HullLab

Data regarding the sample IP.307636 can be accessed here: http://collections.peabody.yale.edu/search/Record/YPM-IP-307636

More information

• DOI: 10.5281/zenodo.167557

Subjects

• Automorph, Microfossil, Foraminifera

Dates

• Publication date: 2016
• Issued: November 19, 2016

Notes

Rights

• https://creativecommons.org/licenses/by/4.0/legalcode Creative Commons Attribution 4.0 International
• info:eu-repo/semantics/openAccess Open Access

Format

electronic resource

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