User Guide#

Welcome to the NexusLIMS User Guide! This guide helps you understand how NexusLIMS works, what to expect from the system, and how to interact with your experimental records.

Want to jump right in?

See the Getting Started page for quick-start installation and configuration instructions.

About This Guide#

This user guide is for:

Microscope users who want to understand how their data is captured and recorded
Facility managers who need to configure and maintain NexusLIMS
Administrators who want to understand the system’s operation and troubleshooting

For developers extending NexusLIMS with new extractors or profiles, see the Developer Guide.

What is NexusLIMS?#

NexusLIMS is an electron microscopy Laboratory Information Management System (LIMS) that automatically generates experimental records by:

Extracting metadata from microscopy data files
Harvesting information from reservation calendar systems (like NEMO)
Building structured XML records conforming to the Nexus Experiment schema
Uploading records to a CDCS (Configurable Data Curation System) frontend

Originally developed at NIST, NexusLIMS is now maintained by datasophos.

Key Features#

Automatic Record Generation: Creates comprehensive experimental records without manual data entry
Multiple File Format Support: Reads metadata from .dm3/.dm4, .tif, .ser/.emi, .spc/.msa files
Standardized Metadata (New in v2.2.0): Uses EM Glossary ontology for field names and units
Schema Validation (New in v2.2.0): Pydantic schemas ensure metadata quality before record building
Calendar Integration: Connects with NEMO lab management systems
Temporal File Clustering: Intelligently groups files into acquisition activities using KDE
CDCS Integration: Publishes records to web-accessible data repositories
Extensible Architecture: Plugin-based extractors and instrument profiles for customization

Understanding NexusLIMS Records#

NexusLIMS automatically creates experimental records that document your microscopy sessions. Each record is a structured XML document that captures:

Who used the instrument (from reservation system)
When the session occurred (start and end times)
What data was collected (files, images, spectra)
How it was collected (instrument settings, metadata)

Record Structure#

Each record contains:

Session Information
- Instrument name and location
- User information (from NEMO reservation)
- Session start and end times
- Project/sample information (if provided)
Acquisition Activities
- Groups of files created together
- Automatically detected from temporal patterns
- Represents distinct experimental tasks
Dataset Metadata
- Technical parameters (voltage, magnification, etc.)
- File information (path, size, creation time)
- Preview images for quick visualization
- Standardized metadata using EM Glossary terminology

Example Record#

Here’s what a typical NexusLIMS record includes:

<Experiment>
  <Summary>
    <Instrument>FEI Quanta 200 ESEM</Instrument>
    <User>jane.smith@example.com</User>
    <StartTime>2025-01-15T09:00:00-05:00</StartTime>
    <EndTime>2025-01-15T11:30:00-05:00</EndTime>
  </Summary>

  <AcquisitionActivity>
    <StartTime>2025-01-15T09:15:00-05:00</StartTime>
    <Dataset>
      <DatasetType>Image</DatasetType>
      <DataType>SEM_Imaging</DataType>
      <Location>sample1_overview_001.tif</Location>
      <Metadata>
        <meta name="Acceleration Voltage" unit="kV">15</meta>
        <meta name="Working Distance" unit="mm">10.2</meta>
        <meta name="Magnification">5000</meta>
        <!-- ... additional metadata ... -->
      </Metadata>
      <PreviewImage>thumbnail_001.png</PreviewImage>
    </Dataset>
    <!-- ... more datasets in this activity ... -->
  </AcquisitionActivity>

  <!-- ... more activities ... -->
</Experiment>

Where Records Are Stored#

Records are uploaded to the NexusLIMS CDCS frontend (a separate web application) where you can:

Search and browse all records
Filter by instrument, date, user, or metadata
View preview images and download original files
Export records in various formats

Common Tasks#

Quick reference for common operations:

Viewing Your Records#

Navigate to the NexusLIMS CDCS web interface (URL provided by your facility)
Log in with your credentials
Use the search interface to find records by:
- Date range
- Instrument name
- Your username
- Metadata fields (e.g., acceleration voltage, magnification)

Ensuring Data is Captured#

To ensure your data is properly captured:

Use the reservation system - Always book instrument time via NEMO
Save files to instrument storage - Use the data saving approach approved by your facility managers
Use standard file formats - Stick to native instrument formats when possible
Provide sample information - Use the reservation notes field for sample details
Use NEMO usage events - Records will only be built for NEMO “usage events” when an instrument is activated

Troubleshooting Common Issues#

Problem	Possible Causes
No record was created for my session	• No files were saved during the session window • Files were saved to incorrect location (outside instrument data path) • Usage event wasn’t properly recorded in NEMO • File modification times don’t fall within session window
Record is missing some files	• Files were created before/after session window • Files are in unsupported format • File permissions prevent access • Files were moved/deleted or timestamps edited before record building
Metadata is incomplete or incorrect	This is normal for some fields: • Some instruments don’t save all metadata to files • Some file formats have limited metadata support • Vendor-specific fields may not be extracted • Warnings in record indicate known unreliable fields

Glossary of Key Terms#

Term	Definition
Acquisition Activity	A group of files created in temporal proximity during a session. Represents a discrete experimental task (e.g., “survey imaging”, “EDS analysis”).
CDCS	Configurable Data Curation System - the web frontend for viewing and searching NexusLIMS records.
Dataset	A single data file (image, spectrum, etc.) with associated metadata.
DatasetType	Classification of data content - one of: Image, Spectrum, SpectrumImage, Diffraction, Misc, Unknown.
EM Glossary	Electron Microscopy Glossary - a community ontology providing standardized field names and definitions.
Extractor	Software component of NexusLIMS that reads microscopy file formats and extracts metadata.
Harvester	Software component of NexusLIMS that polls NEMO for instrument reservations and creates session records.
Instrument Profile	Customization for a specific microscope that modifies metadata extraction behavior.
NEMO	Laboratory scheduling and management system used to track instrument reservations.
Record	An XML document describing a complete experimental session, including all files and metadata.
Session	A period of instrument use corresponding to a NEMO usage event, from start to end time.

Additional Resources#

Getting Help#

Questions about records: Contact your facility administrator
CDCS access issues: Check with your IT department
File format support: See Extractors Documentation
Technical documentation: See Developer Guide

Privacy and Data Management#

What data is collected:

File paths and metadata (technical parameters)
Timestamps and file sizes
Preview images (thumbnails)
User information from NEMO reservations

What is NOT collected:

Raw data file contents (only metadata)
Personal information beyond reservation system data
File contents are not uploaded to CDCS

Data retention:

Records are retained according to facility policy
Original data files are accessed read-only and never modified/edited
Contact your facility about data retention policies