BigStitcher: reconstructing high-resolution image datasets of cleared and expanded samples

Cortical column and whole-brain imaging with molecular contrast and nanoscale resolution

(2019) Ruixuan Gao et al.   SCIENCE

Light sheet theta microscopy for rapid high-resolution imaging of large biological samples

(2018) Bianca Migliori et al.   BMC BIOLOGY

Accurate and fiducial-marker-free correction for three-dimensional chromatic shift in biological fluorescence microscopy

(2018) Atsushi Matsuda et al.   Scientific Reports

Biobeam—Multiplexed wave-optical simulations of light-sheet microscopy

(2018) Martin Weigert et al.   PLoS Computational Biology

Automatic and adaptive heterogeneous refractive index compensation for light-sheet microscopy

(2017) Duncan P. Ryan et al.   Nature Communications

Automatically tracking neurons in a moving and deforming brain

(2017) Jeffrey P. Nguyen et al.   PLoS Computational Biology

MIST: Accurate and Scalable Microscopy Image Stitching Tool with Stage Modeling and Error Minimization

(2017) Joe Chalfoun et al.   Scientific Reports

Protein-retention expansion microscopy of cells and tissues labeled using standard fluorescent proteins and antibodies

(2016) Paul W Tillberg et al.   NATURE BIOTECHNOLOGY

Adaptive light-sheet microscopy for long-term, high-resolution imaging in living organisms

(2016) Loïc A Royer et al.   NATURE BIOTECHNOLOGY

An automated workflow for parallel processing of large multiview SPIM recordings

(2015) Christopher Schmied et al.   BIOINFORMATICS

Clarifying Tissue Clearing

(2015) Douglas S. Richardson et al.   CELL

Nuclear accessibility of β-actin mRNA is measured by 3D single-molecule real-time tracking

(2015) Carlas S. Smith et al.   JOURNAL OF CELL BIOLOGY

Whole-animal functional and developmental imaging with isotropic spatial resolution

(2015) Raghav K Chhetri et al.   NATURE METHODS

BigDataViewer: visualization and processing for large image data sets

(2015) Tobias Pietzsch et al.   NATURE METHODS

Expansion microscopy

(2015) F. Chen et al.   SCIENCE

Efficient Bayesian-based multiview deconvolution

(2014) Stephan Preibisch et al.   NATURE METHODS

Advanced CLARITY for rapid and high-resolution imaging of intact tissues

(2014) Raju Tomer et al.   Nature Protocols

TeraStitcher - A tool for fast automatic 3D-stitching of teravoxel-sized microscopy images

(2013) Alessandro Bria et al.   BMC BIOINFORMATICS

Structural and molecular interrogation of intact biological systems

(2013) Kwanghun Chung et al.   NATURE

Measuring image resolution in optical nanoscopy

(2013) Robert P J Nieuwenhuizen et al.   NATURE METHODS

ImgLib2—generic image processing in Java

(2012) Tobias Pietzsch et al.   BIOINFORMATICS

Elastic volume reconstruction from series of ultra-thin microscopy sections

(2012) Stephan Saalfeld et al.   NATURE METHODS

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

Metadata matters: access to image data in the real world

(2010) Melissa Linkert et al.   JOURNAL OF CELL BIOLOGY

Software for bead-based registration of selective plane illumination microscopy data

(2010) Stephan Preibisch et al.   NATURE METHODS

Globally optimal stitching of tiled 3D microscopic image acquisitions

(2009) S. Preibisch et al.   BIOINFORMATICS

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

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

Tools for neuroanatomy and neurogenetics in Drosophila

(2008) B. D. Pfeiffer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA