# File compatibility and limitations


# Supported files and preparation

ToFScope reads acquisitions from the *TOFWERK* *TOFexplorer*[^1] software in the HDF5 (`.h5`) format. These files may contain stored ion maps or raw events, depending on the analysis history in the vendor software. For raw files without ion maps, the [preparation](../../docs/using-tofscope/raw-preparation.md) process creates a new copy with integrated peak data while retaining raw events and metadata. If the file has missing timing or channel metadata, it requires explicit acknowledgment of reconstruction assumptions.


# Saving files with ToFScope

ToFScope's [Save as](../../docs/using-tofscope/saving-and-exports.md) functionality stores the original acquisition, committed analysis settings, and full-resolution custom results in a new HDF5 file. The original acquisition remains unchanged. ToFScope restores its own analysis metadata, including signals and display settings, when the saved copy is reopened.


# Using a ToFScope file in *TOFexplorer*<sup>[1](#trademark-notice)</sup>

ToFScope attempts to add eligible named signals as vendor peaks and reports any exclusions. Some saved copies have opened in *TOFexplorer*<sup>[1](#trademark-notice)</sup>, but ToFScope analysis names and custom signals may not appear in the vendor interface. ToFScope stores its analysis metadata separately, and the vendor software does not necessarily interpret it.

For a signal made from disjoint mass intervals, vendor peak bounds may span the gaps between intervals. Those bounds do not fully describe the signal; ToFScope retains the exact intervals in its analysis metadata.

> **Warning: Limits of compatibility**
>
> Opening a file in *TOFexplorer*<sup>[1](#trademark-notice)</sup> does not necessarily mean that all metadata is interchangeable or that the applications produce identical numerical results. ToFScope does not claim full interoperability with *TOFexplorer*.


# Current limitations

Live analyses are held in memory and do not survive a service restart unless the data is saved to disk. Shared use requires a trusted authenticated proxy; self-hosted authentication and container deployment remain under development, and NFS deployment has not yet been tested or qualified. The [deployment guide](../../docs/technical-documentation/deployment.md) covers different hosted configurations.

3D rendering is qualitative and uses bounded display previews. The [3D guide](../../docs/using-tofscope/3d-visualization.md) explains pooling, coverage, interpolation, and rendering limits. Profiles, measurements, and CSV exports use original-resolution data.


## Footnotes


[^1]: <span id="trademark-notice"></span>*TOFWERK* and *TOFexplorer* are names owned by [*TOFWERK AG*](https://www.tofwerk.com/). ToFScope is an independent project and is not affiliated with, endorsed by, or sponsored by *TOFWERK AG*.