Version 2023.1.0

Note

The changelog is available at https://gitlab.esrf.fr/tomotools/nabu/-/blob/master/CHANGELOG.md

Highlights

This section highlights some of the available features.

Helical pipeline

Datasets acquired with a helical trajectory are now supported by nabu. A dedicated pipeline has been created, and can be used with the nabu-helical command.

See also: Helical reconstruction

Full-volume cone-beam reconstruction

The full-field pipeline now supports full-volume reconstruction of cone-beam data. Use method = cone (instead of fbp) in [reconstruction]. This feature requires the astra toolbox to be installed, and is still not well-tested.

Volumes stitching

Nabu offers a new command, nabu-stitching, and a new API (nabu.stitching) for performing volumes stitching. It can be used both in pre-processing (assemble projections) and post-processing (assemble reconstructed volumes).

See also: Volumes stitching

Improvements on full-field pipeline

The pipeline got a handful of improvements:

  • Fix binning, binning_z and projections_subsampling which were broken in many cases. These parameters can also be set to arbitrary values.

  • Fix processing margin when using vertical translations and/or CTF

  • Flats distortion correction now works on the GPU backend, but is still very slow

  • Allow to overwrite some metadata, ex. with overwrite_metadata = energy=19kev; pixel_size = 1.6 micron in [dataset]

  • Unsharp mask: add “imagej” mode to have an unsharp similar to the one of ImageJ

  • Add support for .vol output format (mimics the big binary file from PyHST2)

  • Configuration file now supports relative paths