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@quentinblampey quentinblampey released this 20 Jan 17:35
· 66 commits to master since this release
v2.0.0
a972170

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  • API: The Aggregator class has been replaced by a simple function wrapper: sopa.aggregate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
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