https://doi.org/10.5061/dryad.41ns1rnrd

Description of the data and file structure

For the seven specimens scanned we provide the volume of the position on the centroids (x, y, z). This dataset can be run on R using the “foram3D” package from Brombacher et al. (2022). The R package foram3D is freely available for download directly into R from Anieke Brombacher’s GitHub page (https://github.com/AniekeBrombacher/foram3D. )

Files and variables

File: Pulleniatina_Dataset_Volumes.csv

Description: Seven specimens of planktonic foraminifera are listed with taxonomic and volumetric data.

Variables

• Genus
• Species
• Specimen ID
• Chamber n_
• Name
• Voxel count
• Volume (μm3)
• Aspect Ratio
• Center Of Mass X (μm)
• Center Of Mass Y (μm)
• Center Of Mass Z (μm)

Code/software

This dataset can be run on R using the “foram3D” package from Brombacher et alii (2022). The R package “foram3D” is freely available for download directly into R from Anieke Brombacher’s GitHub page (https://github.com/AniekeBrombacher/foram3D).

Following the script published in “Appendix A” within the paper Brombacher et alii, 2022 (https://doi.org/10.5194/jm-41-149-2022), and using the data contained in the dataset provided here (Pulleniatina_Dataset_Volumes_DRYAD.csv), allows to visualize the three dimensional plots and curves.

Access information

Data was derived from the following sources:

• X-ray microscope Zeiss XRADIA Versa 620 
• Volumetric measures and manual segmentation on OSL Dragon fly software.

3D-Volumetric Mesh (.stl)

The software “MeshLab” (https://www.meshlab.net/#download) and “3D-Tool Free Viewer” (https://www.3d-tool.com/en-cad-viewer-download.htm) can be used to import, visualize and manipulate .stl files. 

In “MeshLab”:

• File>Open Project or File>Import Mesh, to open the object (.stl file or 3D volumetric mesh);

• A dialog panel on the side allows the management and view (click on “eye symbol”) of multiple .stl files; in the lower portion of the same panel, the parameters “Shading”, “Color” and “Backface” can be flagged in order to highlight different features of the .stl, modify the colour or the visualization mode;

  Note that the command “Backface” must be in “Double” in order to visualize correctly the .stl; using the command “Color”>”User-Def” a personalised colour can be applied to the object; note that the command “Shading” must be flagged as “Vert” or “Face” to fully visualize the object;

  Further manipulation is possible using the mouse or mousepad via clicking, clicking and dragging the object or scrolling to zoom in and out from the object; note that at maximum magnification (zoom in) the centre of the object view will be located within the object, then allowing to explore/visualize its inner portions;

• After opening the file .stl, Edit>Manipulation Tool, to orient the object;
• File>Measuring Tool, to perform basic linear measurements;

• File>Save Snapshot, to save and export a high definition image of the view, selecting the output folder and with the possibility to modify the background (solid black, gradient etc)

  Detailed tutorials are freely available online (e.g.: https://www.youtube.com/playlist?list=PL8B1E816EAE236B4D) for further guidance.

In “3D-Tool Free Viewer”:

• Open the software, then click on folder symbol (top left) to import the .stl file (3D mesh);
• To manipulate the object use the mouse left click and scroll; right click to activate a secondary menu; to change colour right click on the object>”New color”>select an existing colour or create a new one form the selection palette>”OK”;
• Using the right click on the object select “Transparency ON/OFF” to change the visualization mode of the object;
• From the right panel change “Lighting” and “Background” selecting the colour and moving the yellow dot within the globe icon to redirect the artificial lighting on the surface of the object; further background effects (e.g. 3D effect) can be selected using “Options” from the main menu bar;
• From the top portion of the right panel, under the object’s name, it is possible to see a full list of the components (Part 1, Part n+1) and then to select them or to delete them (selection and then Delete button or right click on the Part you want to erase); all parts can be combined or merged together or can be deleted to obtain a cleaner .stl or to isolate a specific portion;
• To make a cross section of the object click on “Cross Section” in the main menu bar>select the cutting plane (XY. XZ, YZ), adjust the x and z angle dragging the icon, scroll the icon to cross cut; select “side 1” or “side 2” or “cross section” accordingly; clicking on the right icon in this same panel select or deselect “Fill Section”; 
• To save an image of the object: “File”>”Create Picture”>select format (.jpeg/.png), desired resolution, number of views, adjust magnification (zoom) and position of the object>”Create Pic”;

Further free guidance is available online (e.g. https://www.youtube.com/watch?v=0h9PVPFe2oA).