channel-name-parsing

Parse CHANNELNAMES.txt by auto-detecting its format—simple list, cycle-prefixed, tab-separated, or CSV—then extract channel names per cycle. Call load_channel_names(meta_dir) to return a mapping like {1: ["DAPI", "Blank"], 2: ["DAPI", "CD31"]}, ready for downstream labeling in microscopy pipelines.

Format detection handles four conventions: simple lists, cycle-prefixed formats, tab-separated columns, and CSV. The parser auto-identifies the structure, extracts DAPI-based cycle boundaries, handles variable channels per cycle, and ignores comments to produce a consistent cycle-to-channels mapping.

Yes. The parser applies to CODEX-like microscopy data pipelines that output CHANNELNAMES.txt. It auto-detects CODEX and related format conventions, extracts per-cycle channel labels, and returns structured mappings for robust channel labeling downstream.

If the parser cannot detect a supported format or find the file, it returns no result. Fall back to manual channel name definition in your pipeline to ensure labeling continues uninterrupted.

The parser natively handles variable channels per cycle by extracting the full channel list for each detected cycle, preserving structure differences. Each cycle maps to its own channel-name list regardless of length differences between cycles.