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Full 3d coverage into the hands of thousands of biologists

Selective Plane Illumination Microscopy (SPIM) is an emerging imaging technique capable of recording the dynamic developmental events during the formation of animal embryos. The distinguishing feature of SPIM is the ability to record 3d images of the same biological sample from multiple angles thus achieving the full coverage of even relatively large specimen. In order to benefit from this, so called, multi-view SPIM imaging, it is necessary to combine the different angles into a single 3d image, which turns out to be a challenging image analysis problem.

A team of Dresden researchers of the MPI-CBG in collaboration with Carl Zeiss MicroImaging GmbH, Germany developed a novel algorithm that uses small fluorescent beads in the rigid mounting medium as fiduciary markers to achieve fast, precise and completely sample independent registration of multi-view microscopic acquisitions. They provide the method as a fully open-source plugin for Fiji bringing this new solution instantly into the hands of thousands of biologists world-wide. The software libraries behind the plugin contain implementations of many advanced image analysis algorithms that together form a generic platform for matching of partially overlapping point-clouds that can be adapted to other applications.

The open source approach, together with detailed documentation of the principles  and usage of the plugin and the distribution through a widely adopted platform for biological image analysis constitutes a novel paradigm for transferring advances in computer vision to cutting edge biological applications. The Dresden team hopes that other researchers will follow the lead. The algorithm was published in Nature Methods.

Figure legend:
Visualization of the bead-based registration on 8-view SPIM acquisition of the C. elegans worm (left) and 3d rendering of the posterior tip of Drosophila larva reconstructed from 8-view SPIM acquisition (right).