Paste v1.4.0

Updated internal functions to be compatible with POT v0.9.0 package function updates.

PASTE v1.3.0

PASTE v1.3.0

stack_slices_pairwise() and stack_slices_center() now have the ability to return the rotation matrix by specifying input parameter matrix = True.

Also added helper function apply_trsf() to apply a transformation on spatial coordinates using rotation matrix.

Credit to leoguignard for the feature.

PASTE v1.2.2

Fixed bug on previous release that accidentally deleted filter_for_common_genes() function.

PASTE v1.2.1

Improved documentation:

• Cleaned up docstrings.
• Added type-hints.
• Added ReadTheDocs website.

Removed various outdated functions and cleaned up code base.

PASTE v1.2.0

Revamped code and various functions to increase speed.

Code is now backend agnostic.
Added GPU support via Pytorch.
CPU support for Jax, Tensorflow, Pytorch, etc.

PASTE 1.1.4

Bug fix

PASTE 1.1.3

New command line options:

• Rotated coordinates according to alignment and output to files
• Get weights of each spot as input files
• Get initial alignments as input files
• Support for Euclidean distance

PASTE 1.1.2

• Updated lmbda parameter in center_align to have default value if not specified.

• Fixed bug where observation labels were not being transferred from initial to inferred center layer.

• Added warning in center_align for cases where spatial information is not stored as a standard numpy array, which can lead to errors in center_align.

PASTE 1.1.1

• Fixed center align reproducibility bug (gene intersect helper function was previously randomized)
• Added support for scipy sparse matrix format
• Removed deprecated code

PASTE 1.1.0

This newest version of PASTE stores spatial transcriptomics data as an AnnData object. This allows PASTE to be easily integrated with Scanpy. Users can preprocess datasets using Scanpy as well as plot/perform further analysis using Scanpy's spatial data analysis functions.