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References

To get the full benefits of the reader, you can visit and utilize the following tools and platforms.

NOMAD

The reader is fully integrated into the NOMAD research data management platform (a free and open sorce project for data management). In NOMAD, you can find a full example for both the STS as well as the STM reader. The example can be resused to create new uploads and later the uploads can be compared, analyzed, publihsed, and shared with the different colaborators and communities. You can have a look at the NOMAD documentation as well.

NeXus

The reader is using the NXsts (GitHub page) application definition (as a standardized schema) which is developed using the NeXus ontology (GitHub page). To understand the application definition, properly understanding NeXus ontology can be helpful.

STS Reader

The main goal of the STS Reader is to transform different file formats from diverse STS lab into STS community standard STS application definition, community defined template that define indivisual concept associated with STS experiment constructed by SPM community.

STS Example

There are diverse examples for several versions (Generic 5e and Generic 4.5) of the Nanonis software for STS experiments at https://gitlab.mpcdf.mpg.de. But, to utilize that examples one must have an account at https://gitlab.mpcdf.mpg.de. If still you want to try out the examples from the STS reader, please reach out to Rubel Mozumder or the docker container (discussed below).

To get a detailed overview of the sts reader implementation visit pynxtools-stm.

STS docker image

STS docker image contains all prerequisite tools (e.g. jupyter-notebook) and library to run STS reader. To use the image user needs to install docker engine.

STS Image: gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/sts-jupyter:latest

To run the STS image as a docker container copy the code below in a file docker-compose.yaml

# docker-compose.yaml
version: "3.9"
services:
    sts:
        image: gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/sts-jupyter:latest
        ports:
            - 8888:8888
        volumes:
            - ./example:/home/jovyan/work_dir
        working_dir: /home/jovyan/work_dir

and launch the file from the same directory with docker compose up command.