name: instrument-data-allotrope description: Convert laboratory instrument output files (PDF, CSV, Excel, TXT) to Allotrope Simple Model (ASM) JSON format or flattened 2D CSV for LIMS systems and data lakes. type: reference version: 1.0.0 category: science last_updated: 2026-02-03 source: https://github.com/anthropics/knowledge-work-plugins related_skills:

• single-cell-rna-qc
• scvi-tools
• nextflow-pipelines
• clinical-trial-protocol
• scientific-problem-selection capabilities: [] requires: [] tags: [] scripts_exempt: true

Instrument Data Allotrope

Quick Start

# Install requirements first
pip install allotropy pandas openpyxl pdfplumber --break-system-packages

# Core conversion
from allotropy.parser_factory import Vendor
from allotropy.to_allotrope import allotrope_from_file

# Convert with allotropy
asm = allotrope_from_file("instrument_data.csv", Vendor.BECKMAN_VI_CELL_BLU)

Sub-Skills

• Workflow Overview
• Output Format Selection
• Calculated Data Handling
• Validation
• Supported Instruments
• Tier 1: Native allotropy parsing (PREFERRED) (+2)
• Pre-Parsing Checklist
• Common Mistakes to Avoid
• Code Export for Data Engineers
• File Structure
• Example 1: Vi-CELL BLU file (+2)
• Installing allotropy (+2)