thealphacod3r / libertem

Open pixelated STEM framework

LiberTEM is an open source platform for high-throughput distributed processing of large-scale binary data sets using a simplified MapReduce programming model. The current focus is pixelated scanning transmission electron microscopy (STEM) :cite:`doi:10.1002/9783527808465.EMC2016.6284,Ophus_2019` and scanning electron beam diffraction data.

It is designed for high throughput and scalability on PCs, single server nodes, clusters and cloud services. On clusters it can use fast distributed local storage on high-performance SSDs. That way it achieves very high aggregate IO performance on a compact and cost-efficient system built from stock components.

LiberTEM is supported on Linux, Mac OS X and Windows. Other platforms that allow installation of Python 3 and the required packages will likely work as well. The GUI is running in a web browser.

Installation

The short version:

$ virtualenv -p python3.6 ~/libertem-venv/
$ source ~/libertem-venv/bin/activate
(libertem) $ pip install libertem[torch]

Please see our documentation for details!

Deployment as 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.

Applications

• Virtual detectors (virtual bright field, virtual HAADF, center of mass :cite:`Krajnak2016`, custom shapes via masks)
• Analysis of amorphous materials
• Strain mapping
• Custom analysis functions (user-defined functions)
• Off-axis electron holography reconstruction

Please see the applications section of our documentation for details!

The Python API and user-defined functions (UDFs) can be used for more complex operations with arbitrary masks and other features like data export. There are example Jupyter notebooks available in the examples directory. If you are having trouble running the examples, please let us know, either 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. In the future we'd like to implement live acquisition, and more analysis methods for all 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
• Thermo Fisher EMPAD detector :cite:`Tate2016` files
• Quantum Detectors MIB format
• Nanomegas .blo block files
• Gatan K2 IS raw format
• Stacks of Gatan DM3 and DM4 files (via openNCEM)
• FRMS6 from PNDetector pnCCD cameras :cite:`Simson2015` (currently alpha, gain correction still needs UI changes)
• FEI SER files (via openNCEM)
• HDF5-based formats such as Hyperspy files, NeXus and EMD
• Please contact us if you are interested in support for an additional format!

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.