For the past twenty five years the NIH family of imaging software, NIH Image and ImageJ have been pioneers as open tools for scientific image analysis. We discuss the origins, challenges and solutions of these two programs, and how their history can serve to advise and inform other software projects.

Angiogenesis assays based on in vitro capillary-like growth of endothelial cells (ec) are widely used, either to evaluate the effect of anti-and pro-angiogenesis drugs of interest, or to test and compare the functional capacities of various types of EC and progenitor cells. Among the different methods applied to study angiogenesis, the most commonly used is the "endothelial tube formation Assay" (etfA). In suitable culture conditions, EC form two-dimensional (2D) branched structures that can lead to a meshed pseudo-capillary network. An alternative approach to etfA is the "fibrin Bead Assay" (fBA), based on the use of Cytodex 3 microspheres, which promote the growth of 3D capillary-like patterns from coated ec, suitable for high throughput in vitro angiogenesis studies. the analytical evaluation of these two widely used assays still remains challenging in terms of observation method and image analysis. We previously developed the "Angiogenesis Analyzer" for imageJ (AA), a tool allowing analysis of etfA-derived images, according to characteristics of the pseudo-capillary networks. in this work, we developed and implemented a new algorithm for AA able to recognize microspheres and to analyze the attached capillary-like structures from the FBA model. Such a method is presented for the first time in fully automated mode and using non-destructive image acquisition. We detailed these two algorithms and used the new AA version to compare both methods (i.e. ETFA and FBA) in their efficiency, accuracy and statistical relevance to model angiogenesis patterns of Human Umbilical Vein ec (HUVec). Although the two methods do not assess the same biological step, our data suggest that they display specific and complementary information on the angiogenesis processes analysis.

Here, we describe a multigenomic DNA sequence-analysis tool, EVOPRINTER, that facilitates the rapid identification of evolutionary conserved sequences within the context of a single species. The EVOPRINTER output identifies multispecies-conserved DNA sequences as they exist in a reference DNA. This identification is accomplished by superimposing multiple reference DNA vs. test-genome pairwise BLAT (BLAST-like alignment tool) readouts of the reference DNA to identify conserved nucleotides that are shared by all orthologous DNAs. EVOPRINTER analysis of well characterized genes reveals that most, if not all, of the conserved sequences are essential for gene function. For example, analysis of orthologous genes that are shared by many vertebrates identifies conserved DNA in both protein-encoding sequences and noncoding cis-regulatory regions, including enhancers and mRNA microRNA binding sites. In Drosophila, the combined mutational histories of five or more species affords near-base pair resolution of conserved transcription factor DNA-binding sites, and essential amino acids are revealed by the nucleotide flexibility of their codon-wobble position(s). Conserved small peptide-encoding genes, which had been undetected by conventional gene-prediction algorithms, are identified by the codon-wobble signatures of invariant amino acids. Also, EVOPRINTER allows one to assess the degree of evolutionary divergence between orthologous DNAs by highlighting differences between a selected species and the other test species.comparative genomics ͉ evolution ͉ gene structure and function D eciphering the regulatory mechanisms that control coordinate gene expression is a long-standing goal of biology. The comparison of orthologous DNA sequences from multiple vertebrate or invertebrate species promises to identify the cisregulatory elements that are central to the dynamic interplay between a gene and its transcriptional regulators (1-3). This cross-species comparison, termed phylogenetic footprinting, is based on the hypothesis that functionally important sequences evolve at a significantly slower rate than nonfunctional DNA (1). Phylogenetic footprinting has been used successfully to discover multispecies-conserved sequences (MCSs) that are critical for gene function (reviewed in refs. 2, 4, and 5). An essential first step in this process is the alignment of multiple orthologous DNAs. Multisequence-alignment programs include THREADED BLOCKSET ALIGNER (6), FOOTPRINTER (7), CONREAL (5), and PHYME (8). The multiDNA alignments are accomplished either by simultaneous or sequential pairwise alignments of input DNAs, with alignment gaps introduced to optimize the overall homology comparisons.Individual genome searches have also been commonly used to initiate MCS searches, and two popular whole-genome search algorithms are BLAST (9) and BLAT (BLAST-like alignment tool) (10). One significant difference between the BLAST and BLAT algorithms is that BLAT keeps an index of a species genome in memory and uses this index to scan linearly through ...