Marc Jaeger

A new method of three-dimensional computer assisted reconstruction of the developing biliary tract.

A three-dimensional (3-D) computer assisted reconstruction of the biliary tract was performed in human and rat embryos at Carnegie stage 23 to describe and compare the biliary structures and to point out the anatomic relations between the structures of the hepatic pedicle. Light micrograph images from consecutive serial sagittal sections (diameter 7 mm) of one human and 16 rat embryos were directly digitalized with a CCD camera. The serial views were aligned automatically by software. The data were analysed following segmentation and thresholding, allowing automatic reconstruction. The main bile ducts ascended in the mesoderm of the hepatoduodenal ligament. The extrahepatic bile ducts: common bile duct (CD), cystic duct and gallbladder in the human, formed a compound system which could not be shown so clearly in histologic sections. The hepato-pancreatic ampulla was studied as visualised through the duodenum. The course of the CD was like a chicane. The gallbladder diameter and length were similar to those of the CD. Computer-assisted reconstruction permitted easy acquisition of the data by direct examination of the sections through the microscope. This method showed the relationships between the different structures of the hepatic pedicle and allowed estimation of the volume of the bile duct. These findings were not obvious in two-dimensional (2-D) views from histologic sections. Each embryonic stage could be rebuilt in 3-D, which could introduce the time as a fourth dimension, fundamental for the study of organogenesis.

Simple-Graphs Fusion in Image Mosaic: Application to Automated Cell Files Identification in Wood Slices

Results aggregation by disjoint graph merging is potentially a good alternative to image stitching. During the processing of image mosaics, it allows to be free of radiometric and geometric corrections inherent in image fusion. We have studied and developed a generic merging method of disjoint graphs for tracking cell alignments in image mosaics of wood.

Tree branch level of detail models for forest navigation

We present a level of detail (LOD) method designed for tree branches. It can be combined with methods for processing tree foliage to facilitate navigation through large virtual forests. Starting from a skeletal representation of a tree, we fit polygon meshes of various densities to the skeleton while the mesh density is adjusted according to the required visual fidelity. For distant models, these branch meshes are gradually replaced with semi‐transparent lines until the tree recedes to a few lines. Construction of these complete LOD models is guided by error metrics to ensure smooth transitions between adjacent LOD models. We then present an instancing technique for discrete LOD branch models, consisting of polygon meshes plus semi‐transparent lines. Line models with different transparencies are instanced on the GPU by merging multiple tree samples into a single model. Our technique reduces the number of draw calls in GPU and increases rendering performance. Our experiments demonstrate that large‐scale forest scenes can be rendered with excellent detail and shadows in real time.

Stochastic modelling of tree architecture and biomass allocation: application to teak (Tectona grandis L. f.), a tree species with polycyclic growth and leaf neoformation

Background and aims For a given genotype, the observed variability of tree forms results from the stochasticity of meristem functioning and from changing and heterogeneous environmental factors affecting biomass formation and allocation. In response to climate change, trees adapt their architecture by adjusting growth processes such as pre- and neoformation, as well as polycyclic growth. This is the case for the teak tree. The aim of this work was to adapt the plant model, GreenLab, in order to take into consideration both these processes using existing data on this tree species. Methods This work adopted GreenLab formalism based on source-sink relationships at organ level that drive biomass production and partitioning within the whole plant over time. The stochastic aspect of phytomer production can be modelled by a Bernoulli process. The teak model was designed, parameterized and analysed using the architectural data from 2- to 5-year-old teak trees in open field stands. Key results Growth and development parameters were identified, fitting the observed compound organic series with the theoretical series, using generalized least squares methods. Phytomer distributions of growth units and branching pattern varied depending on their axis category, i.e. their physiological age. These emerging properties were in accordance with the observed growth patterns and biomass allocation dynamics during a growing season marked by a short dry season. Conclusions Annual growth patterns observed on teak, including shoot pre- and neoformation and polycyclism, were reproduced by the new version of the GreenLab model. However, further updating is discussed in order to ensure better consideration of radial variation in basic specific gravity of wood. Such upgrading of the model will enable teak ideotypes to be defined for improving wood production in terms of both volume and quality.