Migration guide to sopa>=2.0.0

[quentinblampey]

‼️ sopa 2.0.0 has not been released yet (release date expected in mid-November 2024). This discussion is still a "work in progress"

If you experience issues related to sopa==2.0.0 that are not listed below, please comment below, it can help other users.

New features

• Dask parallelization backend for faster segmentation (useful for API users)
• Spatial elements keys are saved in sdata.attrs so that Sopa knows automatically which element should be used in which function. It is still possible to precise image_key / points_key / shapes_key if needed.
• Allows changing the auto-save settings (i.e. decide if spatial elements are saved on-disk automatically or not)
• Can recover a failed/stopped segmentation when using the API (and also force a segmentation, for Baysor)
• Better cache handling (invisible to API users)
• New tissue segmentation for non-H&E data (sopa.segmentation.tissue)
• Bins aggregation (for VisiumHD-like data)

Snakemake pipeline migration guide

Nothing should change for Snakemake.

API migration guide

• sopa.segmentation.Patches2D is deprecated. Instead, use the functions sopa.make_image_patches or sopa.make_transcript_patches
• Optional arguments of sopa.segmentation.tissue are now more explicit (e.g., blur_kernel_size instead of blur_k).
• The image patches are now called sdata["image_patches"] instead of sdata["sopa_patches"]
• Use sopa.overlay_segmentation instead of sopa.segmentation.overlay_segmentation
• The Aggregator class has been replaced by a simple function wrapper: sopa.aggregate
• The annotations methods are moved to the utils. For instance, use sopa.utils.higher_z_score instead of sopa.annotation.higher_z_score

CLI migration guide

• sopa read has been renamed sopa convert to avoid confusion.
• During segmentation, use --cache-dir-name instead of --patch-dir