HDF5 Data Viewer

The HDF5 viewer opens a projection HDF5 file, shows any image slice (optionally divided by the white field with pixel-shift alignment), and lists the full metadata tree. Useful for sanity-checking a raw dataset before spending GPU time on it.

HDF5 Viewer

Opening a file

In the Batch table, right-click a row → View Data (or the View Data button). The viewer opens in a separate window for that file.

Image tab

  • Normalization — toggle data / data_white

  • Slider — pick the projection index

  • Contrast — Per Image / Min-Max / percentile modes (1–99, 2–98, 5–95) / Manual

  • Shift — arrow keys nudge the white field by 1 px (Shift +1 → 10 px, Ctrl → 50 px). Useful for checking flat-field alignment.

  • Statistics — min / max / mean / std of the current slice.

Metadata tab

  • Attributes — searchable table of every HDF5 attribute with its value and dtype. CSV export.

  • File structure — tree of groups and datasets with shapes / dtypes.

Expected structure

/exchange/data         3D projection stack (required)
/exchange/data_white   3D white field stack  (required for normalisation)

Additional groups under /process, /measurement, /instrument are displayed but not required.

Common failures

File won’t open

Check ls -la and h5ls on the file. Usually permissions or an in-progress write.

Missing /exchange/data or data_white

Not a standard tomography HDF5 layout. Look in the Metadata tab for the actual dataset names.

Slow to navigate

Some datasets have uncompressed per-projection chunks that force a full re-read for every slide. Try the viewer on a binned copy.

See Also