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Version 2026.1.0

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.

New deringers

Two new sinogram-based deringer were added.

Wavelets-median filter

It follows the same principle as the "Munch deringer", although simpler (no Fourier Transforms and less parameters).

To use it in the configuration file: 

[preproc] 
sino_rings_correction = wavelets-median
sino_rings_options = levels=10 ; padding=True # no "signa" parameter here

Variational

This method works by doing a polar transform + variational Gabor filtering. The variational structured noise removal approach is described in

Jerome Fehrenbach, Pierre Weiss, and Corinne Lorenzo, Variational algorithms to remove stationary noise. Applications to microscopy imaging. - https://www.math.univ-toulouse.fr/~weiss/Publis/IEEEIP_VSNR_Final.pdf

To use it in the configuration file: 

[preproc] 
sino_rings_correction = vsnr
sino_rings_options = noise_levels = 15 ; padding=True

Helical pipeline prototype

A prototype of helical reconstruction is available. The entry point is the same:

nabu nabu.conf

Nabu should detect if the input scan is helical (by looking at the vertical translations), and trigger the helical reconstruction if needed.

Automatic delta/beta parameter estimation

A new function to estimate the phase retrieval parameter "delta/beta" was added: nabu.estimation.phase.estimate_delta_beta_from_material().

To use it in the configuration file: 

[phase]
method = paganin # or CTF
delta_beta = auto
material_formula = SiO2
material_density = 2.2

Regularized MLEM reconstruction

The MLEM iterative reconstruction now supports regularization. See the API of [NabuMLEMReconstructor][from nabu.reconstruction.mlem.NabuMLEMReconstructor] for more detail.

To use it from the configuration file:

[reconstruction]
method = mlem
implementation = nabu
iterations = 50
regularization_weight = 0.5

Note that it only works for the nabu implementation (NabuMLEMReconstructor) and not the one based on corrct (CCTMLEMReconstructor).

OME-Zarr output file format

Nabu is now able to save the reconstructions to OME-Zarr file format. It can be written either to disk, or to a remote S3 bucket.

To use it in the configuration file: 

[output]
file_format = ome-zarr
location = https://login:pass@my.server:6780/bucket

Misc and fixes

  • MLEM reconstruction now supports half-acquisition
  • Projection and backprojection operators are now properly normalized: projector
    • Projector is normalized by voxel_size (it was normalized with angular_step before)
    • Backprojector is normalized by angular_step (it was normalized with 1/voxel_size)
  • When reconstructing from a HDF5 file that has multiple entries, into a non-HDF5 output format, the output files will have a suffix corresponding to the current entry. This avoids overwriting the same file with different entries.