---
title: "Instrument Data to Allotrope Converter"
type: skill
id: "knowledge-work-plugins/bio-research/instrument-data-to-allotrope"
category: "Research"
publisher: "Anthropic"
license: "Apache-2.0"
source: "https://github.com/anthropics/knowledge-work-plugins/tree/d900840"
canonical: "https://labs.pho.chat/en/skills/knowledge-work-plugins/bio-research/instrument-data-to-allotrope"
open_in_pho: "https://pho.chat/customize?item=knowledge-work-plugins%2Fbio-research%2Finstrument-data-to-allotrope&utm_source=labs&utm_medium=skill-page&utm_campaign=skills-library"
---

# Instrument Data to Allotrope Converter

Convert laboratory instrument output files (PDF, CSV, Excel, TXT) to Allotrope Simple Model (ASM) JSON format or flattened 2D CSV. Use this skill when scientists need to standardize instrument data for LIMS systems, data lakes, or downstream analysis. Supports auto-detection of instrument types. Outputs include full ASM JSON, flattened CSV for easy import, and exportable Python code for data engineers. Common triggers include converting instrument files, standardizing lab data, preparing data for upload to LIMS/ELN systems, or generating parser code for production pipelines.

Source: Anthropic (Apache 2.0), copied at a pinned commit. Free to use. Part of the Phở Skills library (https://labs.pho.chat/en/skills).
Skill set: Bio research (https://labs.pho.chat/en/skills/knowledge-work-plugins/bio-research.md).

## What it covers
- Workflow Overview
- Quick Start
- Output Format Selection
- Calculated Data Handling
- Validation
- Supported Instruments
- Detection & Parsing Strategy
  - Tier 1: Native allotropy parsing (PREFERRED)
  - Tier 2: Flexible fallback parsing
  - Tier 3: PDF extraction
- Pre-Parsing Checklist
- Common Mistakes to Avoid
- Code Export for Data Engineers
- File Structure
- Usage Examples
  - Example 1: Vi-CELL BLU file
  - Example 2: Request for code handoff
  - Example 3: LIMS-ready flattened output
- Implementation Notes
  - Installing allotropy

## Other skills in this set
- [nf-core Pipeline Deployment](https://labs.pho.chat/en/skills/knowledge-work-plugins/bio-research/nextflow-development.md): Run nf-core bioinformatics pipelines (rnaseq, sarek, atacseq) on sequencing data. Use when analyzing RNA-seq, WGS/WES, or ATAC-seq data—either local FASTQs or public datasets from GEO/SRA. Triggers…
- [Scientific Problem Selection Skills](https://labs.pho.chat/en/skills/knowledge-work-plugins/bio-research/scientific-problem-selection.md): This skill should be used when scientists need help with research problem selection, project ideation, troubleshooting stuck projects, or strategic scientific decisions. Use this skill when users…
- [scvi-tools Deep Learning Skill](https://labs.pho.chat/en/skills/knowledge-work-plugins/bio-research/scvi-tools.md): Deep learning for single-cell analysis using scvi-tools. This skill should be used when users need (1) data integration and batch correction with scVI/scANVI, (2) ATAC-seq analysis with PeakVI, (3)…
- [Single-Cell RNA-seq Quality Control](https://labs.pho.chat/en/skills/knowledge-work-plugins/bio-research/single-cell-rna-qc.md): Performs quality control on single-cell RNA-seq data (.h5ad or .h5 files) using scverse best practices with MAD-based filtering and comprehensive visualizations. Use when users request QC analysis…
- [Bio-Research Start](https://labs.pho.chat/en/skills/knowledge-work-plugins/bio-research/start.md): Set up your bio-research environment and explore available tools. Use when first getting oriented with the plugin, checking which literature, drug-discovery, or visualization MCP servers are…

## Use it
- In Phở: open https://pho.chat/customize?item=knowledge-work-plugins%2Fbio-research%2Finstrument-data-to-allotrope&utm_source=labs&utm_medium=skill-page&utm_campaign=skills-library and press Try, or add it so Phở loads it whenever a request matches. Phở works with your own API key (OpenAI, Anthropic, Google and others).
- Full instructions (original SKILL.md, unchanged): https://labs.pho.chat/skills/raw/knowledge-work-plugins/bio-research/skills/instrument-data-to-allotrope/SKILL.md
- Original files: https://github.com/anthropics/knowledge-work-plugins/tree/d900840 (Apache 2.0).
- Full machine-readable index: https://labs.pho.chat/skills.json