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NUScope

Read, analyze, save and trace electron-microscopy data at the NUANCE Center, Northwestern University.

Created by Roberto dos Reis (@rmsreis) · NUANCE Center, Northwestern University

NUScope is the data layer of the NUScope program. One load() opens any NUANCE microscope file, locally or straight from a Globus collection, and returns calibrated data with one metadata schema for every instrument. Every step after that (analysis, saving, sharing) is recorded as provenance that travels inside the files it writes. Those files are sealed with SHA-256 hashes and signed with your ORCID-linked key, so anyone can check that data, calibration, metadata and history are exactly as you left them.

import nuscope as ns
from nuscope import analyze as an

img = ns.load("Quanta/ResolutionTest_SE_10kx_5kv_008.tif")   # or "globus://<collection-id>/path/file.dm4"
print(img.describe())                                        # instrument, kV, magnification, WD, detector ...
parts = an.particles(an.denoise(img), min_area_nm2=500)       # sizes in nm, with their own provenance
ns.save(img, "result.h5")                                    # HDF5 with metadata, provenance and a seal
print(ns.verify("result.h5"))                                # intact? signed by whom?

  • Read

    Thermo Fisher / FEI, Zeiss, Hitachi and JEOL SEM/FIB images natively; Gatan DM3/DM4, Velox EMD, TIA, Bruker, EDAX, MRC and 30 more through RosettaSciIO.

  • One metadata schema

    Instrument, beam, optics, detector, acquisition and sample, the same for every vendor. The vendor's own metadata is kept untouched.

  • Analyze in physical units

    Noise, denoising, background, FFT and radial profiles, line profiles, particles: in nm, nm² and 1/nm.

  • Tamper-evident provenance

    A hash-chained history, a seal in every file, and Ed25519 signatures tied to your ORCID iD.

  • NUScope Studio

    A browser application for the whole workflow: view, measure, analyze, save, sign and package.

  • Globus and NUANCE-MCP

    Read straight from Globus collections. Let an LLM driving a microscope through NUANCE-MCP save every acquisition as a sealed, signed file.

The NUScope family

Package What it does
NUScope (this package) Reading, metadata, analysis, saving, provenance, integrity, Studio, Globus
NUScope-TOMO FIB-SEM slice-and-view tomography; plugs in as nuscope tomo
EMDataBridge Format standardization and the shared researcher identity (ORCID, signing keys)
NUANCE-MCP Model Context Protocol server for microscope control; loads NUScope and NUScope-TOMO as plugins