> 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/overview.md).

# Overview

### Purpose

CODEX® Processor is a desktop Java application that prepares CODEX® images for downstream data analysis.

![Processor 1.8.3](/files/yMQG2LsSNziWbJkNhN49)

### Core Functionalities

* Provide a user-friendly interface to select datasets and parameters to process
* Prepare raw images for data analysis
  * Align images across cycles
  * Align and stitch tiles across regions
  * Subtract auto-fluorescence
  * Segment and integrate marker intensities for each cell
* Log and output diagnostic data