DOI: 10.5281/zenodo.1169317
title: Calibration Of Test Diameter And Area As Proxies For Body Size In The Planktonic Foraminifera Globoconella Puncticulata

description: Here we provide an extensive image library of<em> Globoconella puncticulata</em>, with accompanying 2D and 3D coordinate data and morphometric measurements.  This data was generated using high-throughput imaging methods (<em>AutoMorph</em>) developed in P.M. Hull's lab at Yale University. This dataset accompanies the manuscript: Brombacher, J.A., Elder, L.E., Hull, P.M., Wilson, P.A. and Ezard, T.H.(In Press) Calibration of test diameter and area as proxies for body size in the planktonic foraminifera <em>Globoconella puncticulata.</em> <em>Journal of Foraminiferal Research</em>. The manuscript describes important details related to data collection and usage and should be consulted before using the data provided here. 

Samples were obtained from three sites in the Atlantic Ocean: equatorial Ocean Drilling Program (ODP) Site 925, subtropical ODP Site 659, and mid-latitude Integrated Ocean Drilling Program (IODP) Site U1313. 1233 individual foraminifera of the species <em>Globoconella puncticulata</em> were picked from these samples to be imaged. Nine slides of microfossils were imaged at multiple focal heights (z-planes; 31.1um step distance) using a light microscope with an automated stage and processed with the image processing models of <em>AutoMorph</em>. <em>AutoMorph</em> software and tutorials can be accessed here: https://github.com/HullLab. For an example of a raw slide scan see: Hsiang, Allison Y., Nelson, Kaylea, Elder, Leanne E., Liu, Yusu, & Hull, Pincelli M. (2016). Slide scan example for Automorph. Zenodo. http://doi.org/10.5281/zenodo.167557. Slides were named with the IODP or ODP site number. Each slide was imaged with the foraminifera arranged in 2-3 orientations (i.e., umbilical, spiral, and/or edge).

One of the nine slide was imaged with both light and computed tomography in order to compare the volumetric data obtained from the two approaches. This slide had 6 individual foraminifera. All individuals imaged with this combination of approaches have ‘CTscan’ included in the file name. This <em>AutoMorph</em>/CT scanned slide was imaged from three orientations (umbilical, spiral, and edge) and with two z-step distances (distance between imaged focal planes on the z-axis) of 11.2 um and 31.31 um.

Images and morphometric data are provided in 9 datasets detailed below. Do note: our slide scanning technique often identifies background light scatter and/or other slide debris (glue, shell fragments, etc.) as ‘objects’, and these objects are numbered in sequence. We have excluded all non-foraminiferal objects from the datasets below, so the object numbers of the foraminifera will often be discontinuous (i.e.: 2,3,4,10,11,16).

<strong>1) 2d_coordinates.tar</strong> provides the 2D coordinates of each successfully extracted orientation from the 1233 individual <em>Globoconella puncticulata</em> (2811 total successfully extracted orientations) in a single csv (all2dcoordinates.csv). 2d_coordinates.tar also provides a csv for each slide scan at a particular orientation (26 slide scans:  4 samples imaged in 3 orientations, 4 samples imaged in 2 orientations, and 1 sample imaged from 3 orientations with two different 2 Z-step sizes per orientations (i.e., 6 scans for the one sample)).

<strong>2) 2dmorph_data_all.tar</strong> contains all <em>Globoconella puncticulata</em> with 2D measurements extracted by the<em> AutoMorph</em> routine run2morph (2811 total successfully extracted orientations), and a text file listing all objects with failed 2D extractions and non-forminiferal objects.

<strong>3) 2d_outline_check.tar</strong> provides an overlay of the extracted 2D outline on the <em>Globoconella puncticulata</em> EDF for quality control purposes for all extracted <em>Globoconella puncticulata</em> (2811 total successfully extracted orientations).

<strong>5) 3d_obj_files.tar</strong> provides directories for each slide scan with the 3D mesh coordinates as obj files for each extracted <em>Globoconella puncticulata</em> (2270 total successfully extracted orientations). Note: more 3D extractions failed than 2D extractions, accounting for the difference in the number of 2D extractions (2811) and 3D extractions (2270).

<strong>6) 3d_pdfs.tar</strong> provides directories of each slide scan with the 3D pdfs of each <em>Globoconella puncticulata</em> extracted (2270 total successfully extracted orientations) for quality control purposes. 3D pdfs, meshes and shape measurements were generated by the <em>AutoMorph</em> module run3dmorph. Note that only some pdf viewers are able to display 3d pdfs properly. 

<strong>4) 3dmorph_data.tar</strong> contains a csv file for each slide scan with the 3d measurements generated for each <em>Globoconella puncticulata</em> by the<em> AutoMorph</em> module run3dmorph (2270 total successfully extracted objects in 26 directories representing each slide scan at a particular orientation).

<strong>7) object_ edf_images.tar</strong> contains the extended depth of focus (EDF)images in 26-directories for each slide scan at a particular orientation. The EDFs are 2D image composites created from the z-stacked photographic images by the <em>AutoMorph</em> focus module. Together, the 26-directories contain 2811 total images representing the successfully extracted 2D orientations.

<strong>8) </strong><strong>sam</strong><strong>pleID.csv</strong> is a csv of all sample information. This includes the Slide name for the physical slide each sample is on, the Object number on that slide scan for each foraminifera used in the study, and the Ocean Drilling Program information for each object. Ocean Drilling Program details consist of the Leg: the Leg number for the drilling cruise, Site: the Ocean Drilling Program collection site number, the Hole:  the drilling hole ID, the Core: the Core number from that drilling site, the core Type: the type of drilling equipment used (H for all these samples which is an advanced hydraulic piston core), the Section: the section number on the core, and the Top and Bottom: the sample top and bottom interval in cm from the top of the section. 

<strong>9) slide_images_boxed.tar</strong> contains one image for each slide view at a particular orientation 26 slide scans:  4 samples imaged in 3 orientations, 4 samples imaged in 2 orientations, and 1 sample imaged from 3 orientations with two different 2 Z-step sizes per orientations (i.e., 6 scans for the one sample). A red box delineates each object extracted using the <em>AutoMorph</em> segment module. Slides are named according to their ocean drilling sample identification (see dataset #10).

<strong>10) z-stacks.tar.gz </strong>contains the original z-stack images of each <em>Globoconella puncticulata </em>(2811 total representing the successfully extracted 2D orientations) in 26 directories representing each slide scan at a particular orientation).
description: AB and THGE are funded by NERC Large Grant NE/P019269/1 and NERC Advanced Research Fellowship NE/J018163/1. AB acknowledges a Johanna M. Resig Foraminiferal Research Fellowship awarded by the Cushman Foundation for Foraminiferal Research. LEE and PMH are funded by the American Chemical Society PRF Grant #55837-DNI8. PAW acknowledges a Royal Society Wolfson Research Merit Award. Samples were provided by the Integrated Ocean Drilling Program (IODP), which is sponsored by the US National Science Foundation and participating countries under management of Joint Oceanographic Institutions, Inc.