LiberTEM/LiberTEM: 0.13.1

Installation

The short version:

$ virtualenv -p python3 ~/libertem-venv/
$ source ~/libertem-venv/bin/activate
(libertem-venv) $ python -m pip install "libertem[torch]"

# optional for GPU support
# See also https://docs.cupy.dev/en/stable/install.html
(libertem-venv) $ python -m pip install cupy

Please see our documentation for details!

Alternatively, to run the LiberTEM Docker image:

$ docker run -p localhost:9000:9000 --mount type=bind,source=/path/to/your/data/,dst=/data/,ro ghcr.io/libertem/libertem

or

$ singularity exec docker://ghcr.io/libertem/libertem /venv/bin/libertem-server

Deployment for offline data processing on a single-node system for a local user is thoroughly tested and can be considered stable. Deployment on a cluster is experimental and still requires some additional work, see Issue #105. Back-end support for live data processing is still experimental as well, see https://github.com/LiberTEM/LiberTEM-live.

Applications

Since LiberTEM is programmable through user-defined functions (UDFs), it can be used for a wide range of processing tasks on array-like data and data streams. The following applications have been implemented already:

• Virtual detectors (virtual bright field, virtual HAADF, center of mass , custom shapes via masks)
• Analysis of amorphous materials
• Strain mapping
• Off-axis electron holography reconstruction
• Single Side Band ptychography

Some of these applications are available through an interactive web GUI. Please see the applications section of our documentation for details!

The Python API and user-defined functions (UDFs) can be used for complex operations such as arbitrary linear operations and other features like data export. Example Jupyter notebooks are available in the examples directory. If you are having trouble running the examples, please let us know by filing an issue or by joining our Gitter chat.

LiberTEM is suitable as a high-performance processing backend for other applications, including live data streams. Contact us if you are interested!

LiberTEM is evolving rapidly and prioritizes features following user demand and contributions. Currently we are working on live data processing, improving application support for sparse data and event-based detectors, performance improvements for GPU processing, and implementing analysis methods for various applications of pixelated STEM and other large-scale detector data. If you like to influence the direction this project is taking, or if you'd like to contribute, please join our gitter chat and our general mailing list.

File formats

LiberTEM currently opens most file formats used for pixelated STEM. See our general information on loading data and format-specific documentation for more information!

• Raw binary files
• NumPy .npy binary files
• Thermo Fisher EMPAD detector files
• Quantum Detectors MIB format
• Nanomegas .blo block files
• Direct Electron DE5 files (HDF5-based) and Norpix SEQ files for DE-Series detectors
• Gatan K2 IS raw format
• Stacks of Gatan DM3 and DM4 files (via openNCEM)
• Single-file Gatan DM4 scans when saved using C-ordering
• FRMS6 from PNDetector pnCCD cameras (currently alpha, gain correction still needs UI changes)
• FEI SER files (via openNCEM)
• MRC (via openNCEM)
• HDF5-based formats such as HyperSpy files, NeXus and EMD
• TVIPS binary files
• Sparse data in Raw CSR (compressed sparse row) format, as is possible to generate from event-based detectors
• Please contact us if you are interested in support for an additional format!

Live processing and detectors (experimental)

See LiberTEM-live!

License

LiberTEM is licensed under GPLv3. The I/O parts are also available under the MIT license, please see LICENSE files in the subdirectories for details.

Acknowledgements

We are very grateful for your continuing support for LiberTEM!

See the acknowledgement page for a list of authors and contributors to LiberTEM and its subprojects. See also our info on funding and industry partners.