As part of Fiji’s sister project - OpenSPIM[1] - we have assembled detailed step-by-step tutorials for SPIMage processing.
- 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.
[1]
Pitrone P. G., Schindelin J., Stuyvenberg L., Preibisch S., Weber M.; Eliceiri K. W., Huisken J., Tomancak P. (2013), “OpenSPIM: an open access light sheet microscopy platform”, Nature Methods **: ,