# 1. Introduction¶

## 1.1. Overview¶

This document contains specifications of the Photon-HDF5 format. This format allows saving single-molecule spectroscopy experiment data in which at least one stream of photon timestamps is present. It has been designed as a standard container format for a broad range of experiments involving confocal microscopy. Examples are confocal smFRET experiments performed with a single or multiple excitation spots. Both μs-ALEX and ns-ALEX data are supported.

## 1.2. What problems are we trying to solve?¶

• Ensuring long term data persistence.
• A disk space and read speed efficient file format for repeated use as well as for archiving.
• Facilitating data sharing and interoperability between analysis programs and research groups.

## 1.3. Features of HDF5¶

• Open-standard: language and platform independent, self-describing format with open source implementations.
• Efficient: the HDF5 format is a binary format that allows compression and fast read/write operations.
• Flexible: data arrays can be stored in “groups” (hierarchical format). Metadata can be attached to each data entry (attributes).
• No limit in data size.
• Support for a variety of numeric and non-numeric data types.

## 1.4. Photon-HDF5: Design principles¶

The main design principles are:

• Simplicity
• Flexibility
• Compatibility

We aim to define a format that has a minimal set of specifications and therefore is easy to implement. At the same time, it is important that the format can be expanded to accommodate new use cases while maintaining backward compatibility.

To achieve simplicity, the only required file characteristics are a general file layout and the presence of a few basic attributes and parameters. The remaining (small set of) fields defined in this document will be present only when needed by a particular measurement.

We retain flexibility by allowing the user to save any arbitrary data outside the specs of this document. To assure that future versions of this format will not conflict with user-defined fields, we require that all user-defined fields be contained in groups called user.