Software

gpCAM: A flexible tool for autonomous data acquisition

Give it a shot: 

• A simple autonomous loop

• An advanced example

Learn more: 

• gpCAM website

• Read the docs

Related Publications:

• Autonomous materials discovery driven by Gaussian process regression with inhomogeneous measurement noise and anisotropic kernels

• A Kriging-Based Approach to Autonomous Experimentation with Applications to X-Ray Scattering

• Gaussian processes for autonomous data acquisition at large-scale synchrotron and neutron facilities

• K-means-driven Gaussian Process data collection for angle-resolved photoemission spectroscopy

• Advances in kriging-based autonomous x-ray scattering experiments

Point of Contact: Marcus Noack

M-TIP: Multitiered iterative phasing

Learn more:

• M-TIP for fluctuation X-ray scattering reconstruction: GitHub Supporting Info

• M-TIP for single-particle diffraction: GitLab

• M-TIP for Coherent Surface Scattering Imaging Reconstruction

Related Publications:

• Iterative phasing for fluctuation X-ray scattering

• Ab initio structure determination from experimental fluctuation X-ray scattering data

• Reconstruction from limited single-particle diffraction data via simultaneous determination of state, orientation, intensity, and phase

• Scaling and Acceleration of Three-dimensional Structure Determination for Single-Particle Imaging Experiments with SpiniFEL

Point of Contact: Jeffrey Donatelli

pyMSDtorch: Easy access to a number of segmentation and denoising methods using convolution neural networks.

Give it a shot: Google Colab

Learn More: Read the docs

Related Publications: see MSDNet below

Point of Contact: Petrus Zwart, Eric Roberts

KSSOLV2.0: A MATLAB solver for Kohn-Sham equations arising from electronic structure calculations

Give it a shot: Download

Learn more: Read the docs

Related Publications:

• KSSOLV 2.0: An efficient MATLAB toolbox for solving the Kohn-Sham equations with plane-wave basis set

• KSSOLV—a MATLAB toolbox for solving the Kohn-Sham equations

• Mesh independence of the generalized Davidson algorithm

• Fast optical absorption spectra calculations for periodic solid state systems

• Interpolative Separable Density Fitting Decomposition for Accelerating Hybrid Density Functional Calculations with Applications to Defects in Silicon

Point of Contact: Chao Yang, Lin Lin

fvGP: Multi-task Gaussian processes

Give it a shot: Google Colab

Learn more: Read the docs

Related Publications:

• Advanced Stationary and Non-Stationary Kernel Designs for Domain-Aware Gaussian

• Exact Gaussian Processes for Massive Datasets via Non-Stationary Sparsity-Discovering Kernels

Point of Contact: Marcus Noack

CovidScreen: Database and deep learning

https://covidscreen.lbl.gov

Give it a shot: Jupyter Notebook

Learn more: Visit the GitHub page 

Related Publications: 

• Validating deep learning inference during chest X-ray classification for COVID-19 screening

• REST Interface Generator (RESTInG)

Point of Contact: Dani Ushizima

 pyCBIR: Search for scientific images using deep learning

Give it a shot: Jupyter Notebook

Learn more: Read the docs

Related Publications:

• Reverse image search for scientific data within and beyond the visible spectrum

• Deep Learning for Cell Image Segmentation and Ranking

Point of Contact: Dani Ushizima

tomoRigidAlign: Rigid Alignment for Tomography

Learn more: Visit the GitHub page

Related Publications: 

• Joint iterative reconstruction and 3D rigid alignment for X-ray tomography

Point of Contact: Kanupriya Pande

tomoCAM: Reconstructing tomography data. Faster!

Learn more: Visit the GitHub page

Related Publications: coming soon

Point of Contact: Dinesh Kumar

LMBML: Lithium metal battery and Machine Learning

Learn more: GitHub page under construction

Related Publications: 

• Lithium Metal Battery Characterization using X-ray Imaging and Machine Learning

• Advancing New Battery Design with Deep Learning

Point of Contact: Dani Ushizima, David Perlmutter 

MSDNet: Mixed-Scale Dense Network

Learn More: Read the docs

Related Publications:

• Improving tomographic reconstruction from limited data using mixed-scale dense convolutional neural networks

• A mixed-scale dense convolutional neural network for image analysis

Point of Contact: Daniël Pelt, James Sethian