Open microscopy is built through collaboration

Open microscopy advances through open and documented interfaces, interoperable data and metadata, reproducible analysis and simulation, and reusable experiment records. Persistent sample identity and coordinate systems can help connect work across instruments, facilities, and software environments.

‍

These foundations also support facility-scale workflows and human-in-the-loop automation and AI, where researchers remain responsible for scientific objectives and approvals. Safe coordination between the microscope, stage, detector, and sample environment becomes increasingly important as workflows become more connected.

How Hummingbird can participate

Hummingbird Scientific can contribute practical knowledge of the physical experiment, including hardware control, sample-environment conditions, controller state, stage coordinates, calibration, synchronization, and safe command boundaries.

‍

Depending on the project, this expertise can support reference experiments, metadata definitions, documented interfaces, customer- or OEM-led integrations, technical documentation, and grant-funded instrument or infrastructure development.

‍

The communities and projects below represent open-source, scientific-computing, and instrument-control efforts relevant to these wider microscopy workflows.

‍

Resources are included for their relevance to open microscopy. Inclusion does not imply affiliation, partnership, endorsement, official support, or verified product compatibility. We welcome corrections and suggestions for additional resources.

‍

Discuss a Collaboration

‍
Suggest a Community Resource

‍

Open-Source TEM Communities

HyperSpy

One of the largest open-source TEM data analysis communities.

Focus:

  • EDS analysis
  • EELS analysis
  • 4D-STEM
  • Spectrum imaging
  • Machine learning workflows

Community:

  • Academic researchers
  • Electron microscopy software developers
  • Materials scientists

Why it matters:

  • Widely used in universities
  • Strong GitHub ecosystem
  • Frequently cited in publications

LiberTEM

Focus:

  • High-speed 4D-STEM processing
  • GPU acceleration
  • Real-time analysis

Community:

  • Detector developers
  • Data scientists
  • 4D-STEM researchers

Why it matters:

  • Strong momentum in next-generation microscopy
  • Open architecture

py4DSTEM

Originally developed around the Berkeley 4D-STEM ecosystem.

‍

Focus:

  • 4D-STEM
  • Strain mapping
  • Ptychography
  • Diffraction analysis

Community:

  • Berkeley Lab
  • University of Washington
  • Cornell
  • National labs

Why it matters:

  • One of the fastest growing TEM software projects

Nion Swift

Focus:

  • STEM image acquisition
  • Live instrument control
  • Data management

Community:

  • Nion users
  • STEM developers
  • Open instrument-control enthusiasts

Why it matters:

  • One of the few open-source acquisition platforms

pyTEMlib

Focus:

  • EELS
  • Spectroscopy
  • Data analysis

Community:

  • Spectroscopy researchers
  • Pycroscopy ecosystem

Pycroscopy

Focus:

  • Scientific imaging
  • Electron microscopy
  • Scanning probe microscopy
  • Machine learning

Community:

  • National labs
  • University research groups

Electron Microscopy Python Communities

Scientific Python Forum

Many TEM developers participate here.

‍

Relevant projects:

  • NumPy
  • SciPy
  • Dask
  • HyperSpy
  • LiberTEM

Jupyter Project

Large number of microscopy workflows are distributed as Jupyter notebooks.

‍

Increasingly becoming the default platform for:

  • TEM automation
  • AI workflows
  • Data analysis

Open Instrument Control Communities

Bluesky Project

Focus:

  • Scientific instrument automation
  • Beamlines
  • Microscopes
  • Experiment orchestration

Community:

  • Synchrotrons
  • National labs
  • Automation researchers

‍

For Hummingbird's FEMTUS vision and automated TEM workflows, this is highly relevant.

EPICS Controls System

Focus:

  • Large-scale scientific instrumentation

Community:

  • National laboratories
  • Synchrotrons
  • Advanced instrumentation groups

TEM User Communities

Center for Open Bioimage Analysis (COBA)

Originally life sciences but increasingly includes EM workflows.

‍

Strong AI community.

GitHub Organizations Worth Following

Organization: HyperSpy GitHub

Focus: EELS, EDS

‍

Organization: LiberTEM GitHub

Focus: 4D-STEM

‍

Organization: py4DSTEM GitHub

Focus: Diffraction

‍

Organization: Nion Software GitHub

Focus: Acquisition

‍

Organization: Pycroscopy GitHub

Focus: Scientific imaging

‍

Organization: OpenNCEM GitHub

Focus: National lab tools