# 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) --- # Agent Instructions: Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter: ``` GET https://help.codex.bio/codex/processor/technical-notes/cycle-alignment.md?ask= ``` The question should be specific, self-contained, and written in natural language. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.