Microscopy of Radiolarians and Foraminiferans Roger C. Wagner, Ph.D. & John R. Jungck, Ph.D
Radiolarians and Foraminiferans are Marine Protozoans consisting of a single cell and a mineral skeleton called a test. These tests are either siliceous (radiolarians) or calcareous (foraminifera). Included in the category of zooplankton, they are carried by the great ocean currents. Fossil tests can be collected from deep ocean drills or recovered from ocean bottoms (radiolarian ooze). The mineralized tests can be viewed by various kings of microscopy and x-ray tomographic scanning devices. They can be modeled three dimensionally and converted into macroscopic representations.
Brightfield Microscopy of Radiolarians-Melding of Stacks of Focal Planes.
Radiolarians can be visualized with light microscopy but a limited depth of field (focus) produces images with blurry outlines due to out-of -focus structure above and below the plane of focus. A solution to this is a process called vertical melding where a through focus series is acquired and vertically melded so that only in focus structure is retained to form the final image. This produces clear, sharp images of radiolarians throughout their depth.
SCANNING ELECTRON MICROSCOPY OF RADIOLARIANS
Scanning electron microscopy affords the greatest resolution when viewing radiolarians. SEM images have an extraordinary depth of field. Specimens can also be rotated to view from several angles. These SEMimages were taken by Debbie Powell in the Imaging Facility of the Delaware Biotechnology Institute.
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Three Dimensional Viewing of Radiolarians with Anaglyphs of SEM Stereopairs
Stereopair images taken with the scanning electron microscope at a 7 degree angle differential are colored with red and cyan and overlayed on a single image. Red-cyan glasses (red on left) will reveal amazing three dimensional perceptions of radiolarians.
Use Red-Cyan Glasses (red on left)
ARTIFICIALLY COLORED RADIOLARIANS
Adobe Photoshop can be used to artificially color images of radiolarians and also give them an artificial texture such as plastic-wrap.This makes them appear wet. Backgrounds can also be created which offset the colors used to paint the images
X-RAY TOMOGRAPHY OF RADIOLARIANS AND FORAMINIFERANS
X-ray tomography is used to visualize the surface and interior structure of solid objects on the basis of their X-ray attenuation (the proportion of x-rays scattered or absorbed as they pass through an object). A tomographic series is acquired by rotating an x-ray source around a specimen and collecting transmitted x-ray intensity on a series of detectors. The detectors record a set of images which are x-ray projections. These are converted to a voxelated 3D file that can be visualized and analyzed with a variety of 3D-based imaging programs. Radiolarians have sliceous (silicon based) tests and Foraminiferans have calcium based tests both of which are x-ray attenuating and provide excellent structure for x-ray tomography. Radiolarians and foraminiferans are exceedingly small (Radiolarians-@ 10um, Foraminiferans-@ 100 um). These 3D files were generated by XRE (X-Ray Engineering), a Belgium company specializing in custom taylored, state-of-the-art X-ray imaging solutions. They specialize in Nano-X-ray tomography which can resolve structure less than a micron.
Thee-Dimensional Modeling of Radiolarians
Tomographic Data sets are a series of x-ray projections. By utilizing a back projection algorithm data points in these projections can be relocated within a volume representing their location in the original specimen. This volume of data can be converted to image stacks (i.e. TIFF, DICOM) consisting of three dimensional volume called voxels. The voxel size is related to the resolution of the acquired data set. Each voxel has an xyz location and a signal intensity. The data sets can be thresholded (setting a voxel intensity) and a surface of the specimen can be generated with three dimensional processing programs such as AMIRA.
Radiolarian "Strew"
Rendered models can be sliced digitally to reveal the internal structure of microfossils. Videos can be generated using a virtual camera to move around the model and even fly into and through the model to view internal structure as if one was actually present there.
If the voxel size is known, precise measurements of the models parameters (volume, surface area) can be calculated. A process called skeletonization (medial axis transform) erodes voxels away leaving only a central row of voxels which represent the essentially geometry of the model. From this skeleton, nodes (connecting points of segments) and segment lengths are readily calculable.
LASER ETCHING RADIOLARIANS AND FORAMINIFERANS IN GLASS
Subsurface laser etching can be used to draw complex 3D data sets inside optically clear glass blocks. A laser delivers enough energy at its focal point to create a small (.1 mm) fracture in the glass, and then is pulsed and repositioned to draw the entire model. Bathsheba Sculpture has produced these beautiful models, and has applied this technique to many types of scientific data.
3D Printing of Radiolarians and Foraminiferans
Three dimensional files of radiolarians and foraminiferans can be generated by x-ray tomography, rendered and converted to a file format which can be used for 3D printing by one of several methods. A standard file format for printing is .stl (standard tesselation language) where a closed surface is defined by polygons (usually triangles) and vertices. Most of the 3D models shown here were printed by "Shapeways"
Light Microscopy of Foraminiferans (verticle melding of focal planes)
Foraminiferans can be visualized by light microscopy but a limited depth of field (focal plane) produces images with blurry outlines due to structure above and below the plane of focus. A solution to this called verticle melding where a through-focus series is acquired and vertically melded so that only in-focus structure is retained to form the final image. This produces clear, sharp images of foraminiferans thoughout their depth.
Scanning Electron Microscopy of Foraminiferans
Scanning Electron Microscopy affords very high resolution when viewing foraminiferans. SEM images have an extraordinary depth of field. Specimens can be rotated for viewing at several angles. These SEM images were taken by Debbie Powell at the Imaging Facility of the Delaware Biotechnology Institute.
THREE DIMENSIONAL MODELING OF FORAMINIFERANS
Foraminiferans are also single-celled organisms (protists) that live primarily in a marine environment. They are somewhat larger than radiolarians and their external skeleton or tests consists of calcium carbonate. These fossil tests are x-ray attenuating and tomographic data sets can be acquired from them. High resolution models can be generated from this data. The models can be examined from any angle and also digitally bisected to reveal the internals structure of the tests. A virtual camera can be scripted to fly around and through the model to examine the interior as if the viewer was actually present there.
Virtual Camera Flythrough of Foraminiferan (Globigerina)
Anaglyph (red cyan) of a Virtual Camera Flythrough of a Foraminifera (Globigerina)
Artificially Colored Foraminifera
Adobe Photoshop can be used to artificially color light micrographs and scanning electron micrographs of forminiferans and also give them an artificial texture such as plastic wrap. This makes them appear wet. Backgrounds can also be created so as to offset the colors used to paint the models.
