Sopa version 2.0.0 This version introduces many new API features but also some breaking changes; check our migration guide to smoothly update your code base. Added Full Visium HD support (including, notably, bins aggregation) Dask parallelization backend for faster segmentation (useful for API users). This can be done via sopa.settings.parallelization_backend = 'dask'. More details in the FAQ. Support for one-line segmentation, e.g. sopa.segmentation.cellpose(sdata, ...) or sopa.segmentation.baysor(sdata, ...). This will implicitly use the selected parallelization backend. 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. More details in the FAQ. Allows changing the auto-save settings (i.e. decide if spatial elements are saved on-disk automatically or not). This can be done via sopa.settings.auto_save_on_disk = False. 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) Full support for baysor>=0.7.0 Added Stardist segmentation (mainly used for H&E data) Added support for Python 3.12 Changes The sopa.io.uniform dataset is now deprecated (use sopa.io.toy_dataset instead) API: The image patches are now called sdata["image_patches"] instead of sdata["sopa_patches"] Breaking changes Drop support for Python 3.9 API: sopa.segmentation.Patches2D is deprecated. Instead, use the functions sopa.make_image_patches or sopa.make_transcript_patches API: Use sopa.overlay_segmentation instead of sopa.segmentation.overlay_segmentation API: The Aggregator class has been replaced by a simple function wrapper: sopa.aggregate API: The annotations methods are moved to the utils. For instance, use sopa.utils.higher_z_score instead of sopa.annotation.higher_z_score CLI: sopa read has been renamed sopa convert to avoid confusion. CLI: during segmentation, use --cache-dir-name instead of --patch-dir Drop support for Python 3.9 Fixes Snakemake path issue on Windows (#64) Issues related to incompatible versions of Baysor