> For the complete documentation index, see [llms.txt](https://stitchit.swcmicroscopy.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://stitchit.swcmicroscopy.com/readme.md).

# StitchIt Documentation

Stitching software for serial-section 2-photon

<div align="center"><img src="https://326914071-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2Fl1mUe85omq3F87GCTSYT%2Fuploads%2Fgit-blob-baa50bf222583d78346df6e065991cb8a662be8a%2Frgb_brain_example.jpg?alt=media" alt="" width="600"></div>

*StitchIt* is the companion package to [BakingTray](http://bakingtray.swcmicroscopy.com): it assembles tiled image data from [BrainSaw microscopes](https://brainsaw.org) into stitched planes.

* See the [Installation](/installation.md) section for setting up a new data analysis PC.
* An overview of the most useful features are detailed on the "[How do I?](/new-users/how-do-i.md)" page. See also the page on [stitching existing data](/advanced-usage/stitching-existing-data.md).
* Those who wish to contribute to the project should see the [contributions](/developers/contributing-code-to-stitchit.md) and [developer notes](/developers/developer-notes.md) pages.