# Overview

### Purpose

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

![Processor 1.8.3](https://1268872846-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2F-LWT7bo4Xbl2jOnmH1yB%2Fuploads%2FzVxacOeKY9p5sBaS5R0y%2FProcessor%20Main%20tab.PNG?alt=media\&token=ef25d162-4da0-4b48-bcb4-2f2b9bc5bdba)

### 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