Calibration of test diameter and area as proxies for body size in the planktonic foraminifera Globoconella puncticulata

<p>Here we provide an extensive image library of<em> Globoconella puncticulata</em>, with accompanying 2D and 3D coordinate data and morphometric measurements.&nbsp; This data was generated using high-throughput imaging methods (<em>AutoMorph</em>) developed in P.M. Hull&#39;s lab at Yale University. This dataset accompanies&nbsp;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>&nbsp;<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.&nbsp;</p> <p>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:&nbsp;https://github.com/HullLab. For an example of a raw slide scan see: Hsiang, Allison Y., Nelson, Kaylea, Elder, Leanne E., Liu, Yusu, &amp; Hull, Pincelli M. (2016). Slide scan example for Automorph. Zenodo. http://doi.org/10.5281/zenodo.167557.&nbsp;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).</p> <p>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 &lsquo;CTscan&rsquo; 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.</p> <p>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 &lsquo;objects&rsquo;, 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).</p> <p><strong>1) 2d_coordinates.tar</strong>&nbsp;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&nbsp;also provides a csv for each slide scan at a particular orientation (26 slide scans:&nbsp; 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)).</p> <p><strong>2) 2dmorph_data_all.tar</strong>&nbsp;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.</p> <p><strong>3) 2d_outline_check.tar</strong>&nbsp;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).</p> <p><strong>5) 3d_obj_files.tar</strong>&nbsp;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).</p> <p><strong>6) 3d_pdfs.tar</strong>&nbsp;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.&nbsp;</p> <p><strong>4) 3dmorph_data.tar</strong>&nbsp;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).</p> <p><strong>7) object_ edf_images.tar</strong>&nbsp;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.</p> <p><strong>8) </strong><strong>sam</strong><strong>pleID.csv</strong>&nbsp;is a csv of all sample information. This includes the&nbsp;Slide name for the physical slide each sample is on, the Object number on that slide scan&nbsp;for each foraminifera used in the study, and the Ocean Drilling Program information for each object. Ocean Drilling Program details consist&nbsp;of the Leg: the Leg number for the drilling cruise, Site: the Ocean Drilling Program collection site number, the Hole: &nbsp;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&nbsp;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.&nbsp;</p> <p><strong>9) slide_images_boxed.tar</strong>&nbsp;contains one image for each slide view at a particular orientation 26 slide scans:&nbsp; 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).</p> <p><strong>10) z-stacks.tar.gz&nbsp;</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).</p>