> 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) --- # Agent Instructions This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com. ## 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, and the optional `goal` query parameter: ``` GET https://help.codex.bio/codex/processor/technical-notes/cycle-alignment.md?ask=&goal= ``` `ask` is the immediate question: it should be specific, self-contained, and written in natural language. `goal` is optional and describes the broader end goal you are ultimately trying to accomplish on behalf of the user. GitBook uses it to tailor the answer towards what is most useful for that goal. 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.