The code and data are both on GitHub. The paper has been published in Wellcome Open Research and has been replicated by multiple other authors.
Metadata annotation is key to reproducibility in sequencing experiments. Reproducing this research using the scripts provided will also show the current level of annotation in years since 2015 when the paper was published.
The current code is written in Torch, which is no longer actively maintained. Since deep learning in nanophotonics is an area of active interest (e.g. for the design of new metamaterials), it is important to update the code to use a more modern deep learning library such as tensorflow/keras
It uses the drake R package that should make reproducibility of R projects much easier (just run make.R and you're done). However, it does depend on very specific package versions, which are provided by the accompanying docker image.