Simple 3D images from fossil and recent micromaterial using light microscopy.

Abstract We present a technique for extracting 3D information from small-scale fossil and Recent material and give a summary of other contemporary techniques for 3D methods of investigation. The only hardware needed for the here-presented technique is a microscope that can perform dark field and/or differential interference contrast with a mounted digital camera and a computer. Serial images are taken while the focus is successively shifted from the uppermost end of the specimen to the lowermost end, resulting in about 200 photographs. The data are then processed almost completely automatically by successive use of three freely available programs. Firstly, the stack of images is aligned by the use of CombineZM, which is used to produce a combined image with a high depth of field. Secondly, the aligned images are cropped and sharp edges extracted with the aid of ImageJ. Thirdly, although ImageJ is also capable of producing 3D representations, we preferred to process the image stack further using osirix as it has the facility to export various formats. One of the interesting export formats is a virtual Quicktime movie file (QTVR), which can be used for documentation, and stereo images can also be produced from this Quicktime VR. This method is easy to apply and can be used for documenting specimens in 3D (at least some aspects) without having to prepare them. Therefore, it is particularly useful as a safe method for documenting limited material, before using methods that may destroy the specimen of interest, or to investigate type material that cannot be treated with any preparatory technique. As light microscopes are available in most labs and free computer programs are easily accessible, this method can be readily applied.

The Rhynie cherts: an early Devonian ecosystem preserved by hydrothermal activity.

The Rhynie cherts contain a remarkable early Devonian terrestrial to freshwater biota preserved in siliceous sinter by the action of a precious-metal-bearing hot spring system. Arthropods, vascular and non-vascular plants, algae, fungi and cyanobacteria are present. Preservation ranges from perfect 3D cellular permineralization to compacted coalified films, and can be related to both silicification processes and stages of biological and physical degradation of the plants at the time of silicification. Plants occasionally have original subaerial vertical axes preserved in growth position, and rhizomes bearing rhizoids. The plant litter of the substrate is also partly silicified. Silicification of organic material took place in hot spring pools, by surface flooding of areas with growing plants, and by permeation of the substrate. Sinters recognized include botryoidal geyserite typical of vent margins, and laminated sinter comparable with that of modern sinter terraces. Massive, vuggy, brecciated and nodular sinter textures are also present. At the microscopic level, textures associated with filamentous elements of the biota, and with the preservation of plants, closely match those present in modern sinters. Oxygen isotope and organic geochemical data from the Rhynie cherts indicate a temperature of 90-120 degrees C. This is apparently greater than the temperature at which elements of the biota were preserved and represents subsequent shallow burial in the hot spring system. The range of temperature and chemistry present at the surface provided high local environmental gradients. Current work attempts to identify thermophilic elements of the biota and document environmental zonation of biota relative to hot spring vents.