> For the complete documentation index, see [llms.txt](https://help.codex.bio/codex/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.codex.bio/codex/processor/technical-notes/cycle-alignment.md).

# Cycle Alignment

Microfluidics, thermal expansion and other temporal effects may perturb the tissue between imaging cycles. To ensure positional consistency for reliable marker expression, tissue displacement is corrected using 3D phase correlation developed by Dr. Stephan Preibisch, Ph.D. at Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG). For each cycle, the nuclear stain pattern is compared to that of the reference cycle, which by default is DAPI of the second cycle. The calculated offsets are used to align all cycles using rigid translation.

[Preibisch, S., Saalfeld, S., & Tomancak, P. (2008, November). Fast stitching of large 3d biological datasets. In Proceedings of the 2nd ImageJ User and Developer Conference, Luxembourg (pp. 7-8).](http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.460.1388\&rep=rep1\&type=pdf)

[GitHub Link](https://github.com/axtimwalde/mpicbg)