Update the README

[adjavon]

Update the README to take into account the pipeline simplification. This should include the following information:

Introduction

2 sentence description of the project and the repository.

Link to the paper:

• Tagged version which was used in the paper (direct link back to a commit)
• Link to adjacent repositories e.g.synistereq

Data Expectations

Describe the kind of data that is considered (volumetric, zarr, etc.)
Describe how the ground truth should look, and be formatted.

Getting started

• Describe how to install e.g. setting up pixi etc.
• Describe how to split the data and what caveats to consider when doing so.
• Describe how to update the configuration for different purposes.
• Describe how to run training and what to expect out of the training loop.
• Describe how to run validation and what to expect out of the validation loop.
• Describe how to run large-scale inference and what to expect out of the inference script.

Acknowledgements

Say who worked on this, when.