MosaicExplorerJ

MosaicExplorerJ stitches 3D tiles from terabyte-scale microscopy datasets organized on a regular two-dimensional grid to reconstruct large lightsheet microscopy volumes of optically cleared samples without prior tile position information or conversion of raw TIFF images into multi-resolution formats.

Key Features:

• Implementation: Implemented as an ImageJ macro that performs 3D tile stitching.
• Data scale and layout: Handles terabyte-scale microscopy datasets arranged on a regular two-dimensional grid.
• Position independence: Performs stitching without requiring prior information about actual tile positions.
• Raw file handling: Operates directly on raw TIFF images without converting them into multi-resolution (pyramid) formats.
• Multichannel support: Supports multiple fluorescence channels for multiplexed imaging data.
• Lightsheet modalities: Accommodates dual-sided lightsheet illumination and dual-sided camera detection.
• Sample compatibility: Designed for lightsheet microscopy datasets derived from optically cleared samples.

Scientific Applications:

• Large-volume reconstruction: Stitch terabyte-scale lightsheet microscopy tiles into contiguous 3D volumes for downstream analysis.
• Cleared-tissue imaging: Reconstruct and analyze 3D morphology of optically cleared biological samples.
• Multichannel analysis: Integrate multiple fluorescence channels for colocalization and multiplexed structural or molecular studies.
• Dual-sided acquisition fusion: Combine datasets from dual-sided illumination and dual-sided camera detection to capture complementary perspectives within a sample.

Methodology:

Implemented as an ImageJ macro that performs 3D tile stitching on tiles arranged in a regular 2D grid, operating directly on raw TIFF files and avoiding the need for prior tile position information or conversion to multi-resolution formats.