labparse

One parser for lab instrument exports. Point it at the file your plate reader, spectrometer, or other bench instrument spat out, and get back a tidy table: one row per reading, with well, row, column, cycle, time in seconds, and value.

import labparse

result = labparse.parse("growth.asc")
result.data            # tidy pandas DataFrame
result.wide()          # one column per well
result.save_csv("tidy.csv")

labparse growth.asc --out tidy.csv
labparse kinetic.txt --wide

The trick: formats are learned once, then free forever

Every instrument exports its own hostile format, and most labs end up writing throwaway parsing scripts for each one. labparse works differently:

1. Known formats parse instantly using bundled recipes, small JSON descriptions of a format that a deterministic engine executes.
2. When labparse meets a format it does not know, it shows the raw file to your own LLM once, and the LLM writes a new recipe.
3. The recipe is only accepted if it actually parses your file. A wrong recipe is rejected and retried, it can never silently produce bad data.
4. Accepted recipes are cached in ~/.labparse/recipes, so each format costs at most one LLM call ever, and cached formats parse offline.

No LLM configured? Everything with a bundled or cached recipe still works, unknown formats give a clear message instead.

Bundled formats

• Tecan plate reader ASCII exports (.asc, repeated well grids)
• Molecular Devices SoftMax Pro / SpectraMax kinetic exports (.txt)
• Generic wide tables, CSV or TSV, with one column per well
• Generic long tables, CSV, with a well column and a value column
• Excel workbooks containing a well header row or a plate grid (pip install labparse[excel])

Recipes are plain JSON. You can read them, edit them, share them with your lab, and drop new ones into the recipe folder. labparse --list-recipes shows everything installed.

Bring your own model (for learning new formats)

labparse looks for a language model in this order and uses the first one it finds:

1. claude CLI (an active Claude Code login)
2. codex CLI
3. ANTHROPIC_API_KEY
4. OPENAI_API_KEY (set OPENAI_BASE_URL for any OpenAI compatible server)

Control it with --llm off, --llm claude, or the LABPARSE_LLM environment variable.

Install

pip install labparse

Excel support: pip install labparse[excel]

Output columns

Extra columns from the instrument, like temperature, are kept.

Author

Built by Paul Crinigan, AI Apps API. Part of the free science tools collection at learnhowtoscience.com.

MIT licensed.