  AtomAI is an open-source software package bridging instrument-specific Python
libraries, deep learning, and simulation tools into a single ecosystem. AtomAI
allows direct applications of the deep convolutional neural networks for atomic
and mesoscopic image segmentation converting image and spectroscopy data into
class-based local descriptors for downstream tasks such as statistical and
graph analysis. For atomically-resolved imaging data, the output is types and
positions of atomic species, with an option for subsequent refinement. AtomAI
further allows the implementation of a broad range of image and spectrum
analysis functions, including invariant variational autoencoders (VAEs). The
latter consists of VAEs with rotational and (optionally) translational
invariance for unsupervised and class-conditioned disentanglement of
categorical and continuous data representations. In addition, AtomAI provides
utilities for mapping structure-property relationships via im2spec and spec2im
type of encoder-decoder models. Finally, AtomAI allows seamless connection to
the first principles modeling with a Python interface, including molecular
dynamics and density functional theory calculations on the inferred atomic
position. While the majority of applications to date were based on atomically
resolved electron microscopy, the flexibility of AtomAI allows straightforward
extension towards the analysis of mesoscopic imaging data once the labels and
feature identification workflows are established/available. The source code and
example notebooks are available at https://github.com/pycroscopy/atomai.
