Atlas Free Slice Alignment Pipeline¶

slice_alignment.main()[source]¶

Perform atlas-free slice alignment of a set of images

Parameters:¶

outdirstr: The directory where all intermediate and final outputs should be saved
-fnameslist of str: The list of all files to be registered in
-npadint: TODO
-downint: TODO
-afloat: TODO
-pfloat: TODO
-niter_big_loopint: TODO
-niter_regint: TODO
-niter_atlasint: TODO
-asquarefloat: TODO
-asquare0float: TODO
-anisotropy_factorfloat: TODO
-epTfloat: TODO
-epLfloat: TODO
-epvfloat: TODO
-cfloat: TODO
-sigmaMfloat: TODO
-sigmaRfloat: TODO
-a_regfloat: TODO
-devicestr: Default - cpu; The device where PyTorch computations should be performed
-dtypestr: Default - float; The dtype used for PyTorch computations
–enable_deformationbool: TODO: NOT CURRENTLY SUPPORTED
–remove_artifactsbool: If present, remove rows or columns containing exclusively 1s. This type of artifact is common in certain use cases.
–saveAllFigsbool: If present, save all potential figures into ‘outdir’