NexusLIMS#

NexusLIMS
An automated Laboratory Information Management System for electron microscopy

NexusLIMS automatically generates experimental records by extracting metadata from microscopy data files and harvesting information from laboratory calendar systems.

Key Features#

  • Automated Record Building - Automatically build metadata records for electron microscopy experiments, with metadata extraction from proprietary formats, preview image generation, and more!

  • Facility Management Integration - NexusLIMS integrates with the NEMO lab management system for harvesting of experimental sessions and instrument information.

  • Multi-Destination Export Framework - Configurable plugin-based export system supporting multiple data repositories, including NexusLIMS CDCS as the primary destination and the eLabFTW electronic lab notebook. NexusLIMS can easily be extended for support of custom destinations.

  • Comprehensive support for common Electron Microscopy file formats - NexusLIMS extracts detailed metadata from DigitalMicrograph DM3/DM4 files, FEI/Thermo TIF images, Tescan TIF images, Zeiss TIF images, FEI TIA (.ser/.emi), EDAX (.spc/.msa) EDS spectra, and more

  • Temporal File Clustering - Intelligent grouping of files into Acquisition Activities based on temporal analysis (with customizable sensitivity)

  • Extensible Architecture - Plugin-based extractor system and instrument profiles for easy customization

  • Structured XML Records - Standards-compliant records with comprehensive session and technical metadata

  • Metadata Standardization - Emerging standardization using EM Glossary terms and Pydantic validation (work in progress)

  • Physical Unit Management - Automatic normalization of physical quantities (voltages, distances, times) to preferred units via Pint

📸 Screenshots

Click here to see screenshots of the user-facing frontend and its features.

Screenshot Gallery
🚀 Getting Started

New to NexusLIMS? Start here for installation, configuration, and quick start guide.

Getting Started
🔄 Migration Guide

Upgrading from v1.x? Step-by-step instructions for migrating to v2.0+.

Migration Guide
📖 User Guide

Learn about the record building workflow and data taxonomy.

User Guide
🛠️ Supported File Formats

Explore the comprehensive list of supported microscopy file formats and NexusLIMS’s metadata extraction capabilities.

Extractors
⌨️ Developer Guide

Understand the architecture, database design, and how to extend NexusLIMS.

Dev Guide
📚 API Reference

Complete API documentation and changelog.

Reference
🖥️ Frontend Web Interface

Documentation about deployment and management of the CDCS web frontend for searching and visualizing records.

Frontend Guide
💼 Need Help with NexusLIMS?

Datasophos offers professional services for NexusLIMS:

  • 🚀 Deployment & Integration - Get NexusLIMS running in your lab with expert configuration

  • 🔧 Custom Development - Extend NexusLIMS with custom extractors, harvesters, or workflows

  • 🎓 Training & Support - Onboard your team and get ongoing technical support

Ready to streamline your microscopy data management?

Contact Datasophos

On this page

This Page