Quantitative comparison of taxa and taxon concepts in the diatom genus Fragilariopsis: a case study on using slide scanning, multiexpert image annotation, and image analysis in taxonomy.

Semiautomated methods for microscopic image acquisition, image analysis, and taxonomic identification have repeatedly received attention in diatom analysis. Less well studied is the question whether and how such methods might prove useful for clarifying the delimitation of species that are difficult to separate for human taxonomists. To try to answer this question, three very similar Fragilariopsis species endemic to the Southern Ocean were targeted in this study: F.

Culture of human neurospheres in 3D scaffolds for developmental neurotoxicity testing.

Human neural progenitor cells cultured as neurospheres are a promising tool for developmental neurotoxicity testing in vitro. In order to obtain a human cell-based tissue culture system as close to the organ as possible, it is desirable to improve the spatial organization of the "Neurosphere Assay" and use 3D scaffolds to better mimic the in vivo three dimensional cell microenvironment. For this reason we have established the conditions for short-term culture (up to 6 days) in matrigel or in IKVAV-3 peptide-functionalized hydrogels, and for long-term culture (>25 days) in IKVAV-3 peptide-functionalized hydrogels showing that these conditions support human neural progenitor cells' migration, differentiation to neurons and formation of neuronal networks.

PROCESS FLOW FOR CLASSIFICATION AND CLUSTERING OF FRUIT FLY GENE EXPRESSION PATTERNS.

The rapidly growing collection of fruit fly embryo images makes automated Image Segmentation and classification an indispensable requirement for a large-scale analysis of in situ hybridization (ISH) - gene expression patterns (GEP). We present here such an automated process flow for Segmenting, Classification, and Clustering large-scale sets of Drosophila melanogaster GEP that is capable of dealing with most of the complications implicated in the images.

FeatureScan: revealing property-dependent similarity of nucleotide sequences.

FeatureScan is a software package aiming to reveal novel types of DNA sequence similarity by comparing physico-chemical properties. Thirty-eight different parameters of DNA double strands such as charge, melting enthalpy, conformational parameters and the like are provided. As input FeatureScan requires two sequences, a pattern sequence and a target sequence, search conditions are set by selecting a specific DNA parameter and a threshold value.