instrument-data-allotrope

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	"2026-02-03T00:00:00.000Z"
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)