Squidpy 1.1.0 (2021-07-01)

Bugfixes

• Fix squidpy.im.ImageContainer to work with different scaled #320.

• Fix handling of anndata.AnnData.obsm in squidpy.im.ImageContainer.interactive() #335.

• Fix Z-dimension in squidpy.im.ImageContainer.interactive() #351.

• Fix plotting bug in squidpy.pl.ripley() #352.

• Fix handling of NaNs in squidpy.gr.ligrec() #362.

Features

• Add many new tutorials and examples

• Add squidpy.gr.sepal() [Anderson and Lundeberg, 2021] #313.

• Replace squidpy.gr.moran with squidpy.gr.spatial_autocorr(), which implements both Moran’s I and Geary’s C #317.

• Add option to compute graph from Delaunay triangulation in squidpy.gr.spatial_neighbors() #322.

• Add lazy computation using dask for squidpy.im #324.

• Allow Z-dimension shared across all layers in squidpy.im.ImageContainer #329.

• Replace squidpy.gr.ripley_k with squidpy.gr.ripley() #331

• Generalize graph building in squidpy.gr.spatial_neighbors() #340.

• Add 3 new example datasets #348:

  • squidpy.datasets.merfish()

  • squidpy.datasets.mibitof()

  • squidpy.datasets.slideseqv2()

• Enable additional layer specification in squidpy.im.calculate_image_features() #354.

• Expose canvas_only in squidpy.pl.Interactive.screenshot() #363.

• Various minor improvements to the documentation #356, #358, #359.