2013-06-18 - SPIMage processing tutorials

Integral part of SPIM imaging is data processing sometimes referred to as SPIMage processing. The OpenSPIM project relies on tight integration with Fiji where most of the algorithms for SPIMage processing have been implemented in the past.

We have assembled extensive tutorials that will walk you through all the steps required to put multi-view SPIM data together.


 * We start by defining System requirements and downloading '''sample OpenSPIM data,
 * followed by optional pre-processing steps.
 * Multi-view registration is at the heart of SPIMage processing pipeline.
 * Multi-view Fusion section discusses how to combine several view into one output image
 * Time series registration removes the sample drift across long-term timelapse.

The pipeline is relatively linear as described above, we highlight the steps where alternative routes exist.

Theoretical principles of the methods involved are best described on the SPIM pages of Fiji wiki.

The description of several steps of the SPIMage processing pipeline are still in the works. Particularly Multi-view deconvolution, data viewing and 3D rendering. Stay tuned.