NexusLIMS
NexusLIMS is a
peer-reviewed, open-source
Laboratory Information Management System (LIMS) that automatically
generates experimental records for shared-use electron microscopy
facilities. It extracts metadata directly from instrument data files
(e.g. .dm3/.dm4, .tif, .ser/.emi, and others) and combines it
with reservation and usage information harvested from a facility’s
scheduling system (e.g. NEMO) to
build structured, searchable experiment records, all without requiring
any manual data entry from researchers. This enables facilities to
generate FAIR data as a
natural byproduct of their existing workflows.
I originally designed, built, and deployed NexusLIMS while at NIST, where it has been used in production since 2020 across dozens of electron microscopes and associated spectrometers. Since leaving NIST in 2025 and founding Datasophos, I’ve continued developing the project as an independent, open-source fork (not affiliated with NIST), sponsored in part by the Singh Center for Nanotechnology at the University of Pennsylvania. This next-generation v2.0 release includes:
- A modern, flexible plugin architecture for metadata extraction, making it much easier to add support for new instrument and file types
- Drastically simplified deployment and configuration, lowering the barrier for other facilities to adopt the system
- Support for exporting records to multiple data repository destinations
- Extensions of the (NexusLIMS-CDCS) frontend for searching, filtering, editing, annotating, and exploring experiment records
NexusLIMS is fully open source under the MIT license (using Python), with full documentation available here and a live demo available here. See the datasophos/NexusLIMS repository for source code and more details, or datasophos.co/nexuslims for more information on deployment, customization, training, and consulting services.