channel-name-parsing
Installation
SKILL.md
Channel Name Parsing - Research Notes
Experiment Overview
| Item | Details |
|---|---|
| Date | 2024-12-15 |
| Goal | Parse channel names from various CHANNELNAMES.txt formats |
| Environment | KINTSUGI pipeline, Python 3.10+ |
| Status | Success |
Context
Different microscopy systems and users produce CHANNELNAMES.txt files in various formats. KINTSUGI needs to parse channel/marker names to label output files correctly. The parsing must auto-detect the format and handle multiple conventions.
Supported Formats
Format 1: Simple List (One Channel Per Line)
Most common format from CODEX systems. Each line is a channel name, 4 channels per cycle. Cycle number extracted from DAPI marker name (DAPI-01, DAPI-02, etc.).