ViBE-Z: a framework for 3D virtual colocalization analysis in zebrafish larval brains

BrainAligner: 3D registration atlases of Drosophila brains

(2011) Hanchuan Peng et al.   NATURE METHODS

In vivo protein trapping produces a functional expression codex of the vertebrate proteome

(2011) Karl J Clark et al.   NATURE METHODS

Scale: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain

(2011) Hiroshi Hama et al.   NATURE NEUROSCIENCE

Comprehensive catecholaminergic projectome analysis reveals single-neuron integration of zebrafish ascending and descending dopaminergic systems

(2011) Tuan Leng Tay et al.   Nature Communications

Three-Dimensional Reconstruction of Brain-wide Wiring Networks in Drosophila at Single-Cell Resolution

(2010) Ann-Shyn Chiang et al.   CURRENT BIOLOGY

Harmonic Filters for 3D Multichannel Data: Rotation Invariant Detection of Mitoses in Colorectal Cancer

(2010) Matthias Schlachter et al.   IEEE TRANSACTIONS ON MEDICAL IMAGING

Visualization of image data from cells to organisms

(2010) Thomas Walter et al.   NATURE METHODS

Analysis of Cell Fate from Single-Cell Gene Expression Profiles in C. elegans

(2009) Xiao Liu et al.   CELL

Emx3 is required for the differentiation of dorsal telencephalic neurons

(2009) Gudrun Viktorin et al.   DEVELOPMENTAL DYNAMICS

Arcuate nucleus expression of NKX2.1 and DLX and lineages expressing these transcription factors in neuropeptide Y+, proopiomelanocortin+, and tyrosine hydroxylase+neurons in neonatal and adult mice

(2009) Cindy L. Yee et al.   JOURNAL OF COMPARATIVE NEUROLOGY

XuvTools: free, fast and reliable stitching of large 3D datasets

(2009) M. EMMENLAUER et al.   JOURNAL OF MICROSCOPY

A 3D digital atlas of C. elegans and its application to single-cell analyses

(2009) Fuhui Long et al.   NATURE METHODS

Automated high-throughput mapping of promoter-enhancer interactions in zebrafish embryos

(2009) Jochen Gehrig et al.   NATURE METHODS

Performance vs computational efficiency for optimizing single and dynamic MRFs: Setting the state of the art with primal-dual strategies

(2008) Nikos Komodakis et al.   COMPUTER VISION AND IMAGE UNDERSTANDING

Dense image registration through MRFs and efficient linear programming☆

(2008) Ben Glocker et al.   MEDICAL IMAGE ANALYSIS

Visualization of monoaminergic neurons and neurotoxicity of MPTP in live transgenic zebrafish

(2007) Lu Wen et al.   DEVELOPMENTAL BIOLOGY

Adaptive correction technique for 3D reconstruction of fluorescence microscopy images

(2007) Y.Q. Guan et al.   MICROSCOPY RESEARCH AND TECHNIQUE