(A) Maximum projection of a 5-channel confocal 3D image of a 100 μm thick section of rat hippocampus. Red: GFAP-labeled astrocytes; green: EBA-labeled blood vessels; yellow: Iba1-labeled microglia; cyan: CyQuant-labeled cell nuclei; purple: NeuroTrace-labeled Nissl substance; scale bar=50 μm. (B) 3D rendering (with a similar color scheme) of the segmented and classified cells produced using the FARSIGHT techniques for (A). Image courtesy of Badrinath Roysam (Bjornsson et al., 2008)

Maximum projection of 3D registered and overlaid neuronal patterns of multiple fruit fly central complexes (top) and thoracic ganglia (bottom), each with a different GAL4 line (Peng et al., unpublished data). Red: a205; Green: EB1; Cyan: NP2320; Yellow: NP6510; gray: NC82-labeled neuropil. Raw confocal images were produced by Julie Simpson and Phuong Chung.

Clustering analysis of embryonic in situ mRNA gene expression patterns of fruit fly genes and its utility in assisting prediction of the regulatory sequence motifs. Based on clustering the eigen-embryo profiles (purple–cyan plot) of representative gene expression patterns, four genes in S_Q are detected to be co-expressed genes. This prediction is consistent with their known gene regulation relationship for fly mesoderm patterning. Further, S_Q can be used to predict sequence motifs. The motif example shown is detected using the entire upstream regions of the homologous genes in eight fly species D.melanogaster, D.simulans, D.yakuba, D.erecta, and D.ananassae, D.pseudoobscura, D.virilis, and D.mojavensis, along with three randomly selected example genes in the subsequent genome-wide motif scanning results. BDGP (fruitfly.org) ISH images (in blue) and annotations are also shown, without image cropping or orientation correction. Short terms of annotations: AAISN, amnioserosa anlage in statu nascendi; AISN, anlage in statu nascendi; AEA, anterior endoderm anlage; AEAISN, anterior endoderm anlage in statu nascendi; CB, cellular blastoderm; DEA, dorsal ectoderm anlage; DEAISN, dorsal ectoderm anlage in statu nascendi; EAISN, endoderm anlage in statu nascendi; FA, foregut anlage; FAISN, foregut anlage in statu nascendi; HMA, head mesoderm anlage; HA, hindgut anlage; MAISN, mesoderm anlage in statu nascendi; PTEA, posterior endoderm anlage; S, subset; TMA, trunk mesoderm anlage; TMAISN, trunk mesoderm anlage in statu nascendi; VEA, ventral ectoderm anlage; VNA, ventral neuroderm anlage. Original image source: (Peng et al., 2007)