OptiJ

OptiJ provides optical projection tomography (OPT) for three-dimensional imaging of mesoscopic cleared biological specimens to enable quantitative morphological and anatomical analysis.

Key Features:

• Imaging capabilities: Visible-light OPT of transparent specimens up to 13 mm in height and 8 mm in depth with ~50 µm resolution.
• ImageJ plugin library: Software components implemented as ImageJ plugins for OPT data reconstruction and analysis.
• Advanced correction routines: Algorithms to correct uneven illumination and sample jitter during reconstruction.
• Accelerated reconstruction: Support for CPU and GPU-accelerated tomographic reconstruction.
• Modular hardware and software design: Hardware and software components are modular to permit customization and further development.
• Off-the-shelf optical components: System built from commercially available optical components.

Scientific Applications:

• Cleared murine lung lobe imaging: Three-dimensional imaging and reconstruction of cleared lung lobes from adult mice for anatomical analysis.
• Biomedical phenotyping: Morphological phenotyping of mesoscopic biological specimens.
• Small-animal anatomical studies: Detailed anatomical studies in small animal models at organ and tissue scales.
• Developmental and pathology studies: Visualization of organ structures for developmental biology, disease pathology, and phenotypic variation analysis.

Methodology:

Computational methods comprise an ImageJ plugin library for OPT data reconstruction and analysis, correction algorithms for uneven illumination and sample jitter, and support for CPU- and GPU-accelerated tomographic reconstruction.