Instrument Data Converter
Convert lab instrument files to Allotrope ASM format with automated validation
Every instrument in your lab exports data in its own proprietary format. Your plate reader, spectrophotometer, and qPCR system each speak a different language, and standardizing them for analysis or submission means hours of manual reformatting.
Who it's for: lab scientists standardizing data from multiple instruments, bioinformaticians building data pipelines for lab equipment, pharmaceutical companies adopting Allotrope standards, quality teams ensuring instrument data compliance, researchers tired of manually reformatting instrument output
Example
"Convert our plate reader and qPCR data to Allotrope ASM format" → Automated conversion pipeline parsing native instrument files, mapping to ASM schema, validating against standards, and producing compliant output — with error reports for any data that doesn't conform
CLAUDE.md Template
New here? 3-minute setup guide → | Already set up? Copy the template below.
npx ccplaybooks add instrument-data-converter# Instrument Data to Allotrope Converter
Convert instrument files into standardized Allotrope Simple Model (ASM) format for LIMS upload, data lakes, or handoff to data engineering teams.
> **Note: This is an Example Workflow**
>
> This workflow demonstrates how automated assistants can support your data engineering tasks -- automating schema transformations, parsing instrument outputs, and generating production-ready code.
>
> **To customize for your organization:**
> - Modify the `references/` files to include your company's specific schemas or ontology mappings
> - Use an MCP server to connect to systems that define your schemas (e.g., your LIMS, data catalog, or schema registry)
> - Extend the `scripts/` to handle proprietary instrument formats or internal data standardsGet new playbooks like this one
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What This Does
Converts instrument files from cell counters, spectrophotometers, plate readers, qPCR systems, and more into standardized Allotrope Simple Model (ASM) format. Supports native parsing via allotropy library, flexible fallback parsing, and PDF extraction — with validation against ASM schemas.
Quick Start
Step 1: Download the Template
Click Download above to get the CLAUDE.md file.
Step 2: Install Dependencies
pip install allotropy pandas openpyxl pdfplumber
Step 3: Start Working
claude
Say: "Convert this cell counting data to Allotrope format"
Supported Instruments
| Category | Instruments |
|---|---|
| Cell Counting | Vi-CELL BLU, Vi-CELL XR, NucleoCounter |
| Spectrophotometry | NanoDrop One/Eight/8000, Lunatic |
| Plate Readers | SoftMax Pro, EnVision, Gen5, CLARIOstar |
| ELISA | SoftMax Pro, BMG MARS, MSD Workbench |
| qPCR | QuantStudio, Bio-Rad CFX |
| Chromatography | Empower, Chromeleon |
Output Formats
- ASM JSON — Full semantic structure with ontology URIs (for LIMS, data lakes)
- Flattened CSV — 2D tabular format (for Excel, quick analysis)
- Python parser code — Standalone script for data engineer handoff
Parsing Strategy
- Native allotropy (preferred) — Try allotropy library first for supported vendors
- Flexible fallback — Column name fuzzy matching, unit extraction from headers
- PDF extraction — Extract tables using pdfplumber, then apply fallback parsing
Tips
- Always validate ASM output before delivering — run the validation script
- Separate raw measurements from calculated/derived values
- When unsure about field mapping, ask for clarification rather than guessing
- Check
references/supported_instruments.mdfor the complete instrument list
Example Prompts
"Convert this cell counting data to Allotrope format"
"Parse this NanoDrop CSV and generate ASM JSON"
"Flatten this ASM file into a CSV for Excel"
"Generate a standalone parser script for Vi-CELL BLU files"