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[2.0.3] - xxxx-xx-xx

[2.0.2] - 2025-02-21

Added

  • Added H-optimus-0 model for H&E patches embeddings @stergioc (#208)
  • Can provide qv_threshold argument to the Xenium reader to filter low quality transcripts @callum-jpg (#210)

Changed

  • Storing patches embeddings as an AnnData object instead of images (#212) (see updated tuto)

Fixed

  • Right sorting scales for WSI reader with openslide backend @stergioc (#209)
  • When a polygon cannot be simplified (for the Xenium Explorer), convert it to a circle (#206)
  • sopa explorer write: use correct default argument for table_key in the CLI (#211)
  • Fix Baysor usage on Windows (#185)
  • Fix tight patches returning a different number of patches (#214)

[2.0.1] - 2025-02-10

Fixed

  • Safer check dataframe series is of integer dtype (#179)
  • Ensure feature_key is converted correctly to a string (#185)
  • Fixed the WSI readers @stergioc (#192)
  • Fixed points_key usage in sopa.aggregate (#194)

Added

  • Aggregation and segmentation now exclude non-interesting gene names (e.g., "blank", "unassigned", ...) (#144)
  • Can filter low-quality transcript for transcript-based segmentation (#79)
  • Possibility to choose the table name for the report (#183)
  • Possibility to choose the table name for sopa.io.explorer.write (#183)
  • Can set all spatialdata_io.xenium arguments in sopa.io.xenium
  • CLI for stardist @jeffquinn-msk (#189)
  • Baysor logs if running on one patch, and return the right error code in CLI @jeffquinn-msk (#199)
  • Baysor parallelization per patch @Marius1311 (#203)

Changed

  • sopa.io.write_report is copying the adata to avoid modifying it (#196)

[2.0.0] - 2025-01-20

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

[1.1.6] - 2024-11-29

Fix

  • Support baysor>=0.7.0 (#125, @lguerard).
    • NB: For Snakemake, please remove the new_component_* arguments from the Baysor config.
  • Use DataTree from xarray - use new spatialdata version (#159)

[1.1.5] - 2024-09-17

Fix

  • Accept object dtype for channel names (#114)

Changed

  • Update MACSima reader to read the channel names of the latest file format

[1.1.4] - 2024-08-21

Hotfix

  • Fixed Baysor issue on MERSCOPE data with the Vizgen prior
  • Fix patch-maker issue due to new API temporary implementation

[1.1.3] - 2024-08-18

Fix

  • Fixed aggregation issue when gene names are NaN or None (#101)
  • Fix Xenium reader for old Xenium data format (#105)

Added

  • Support multipolygons in ROI rasterization
  • Added bins aggregation
  • Added Visium HD reader (tutorial coming soon)

Changed

  • Import submodules in init (segmentation, io, utils)
  • API simplification in progress (new API + tutorial coming soon)

[1.1.2] - 2024-07-24

Fix

  • Convert intensities values in integer for the ome_tif and aicsimageio readers
  • Fix cellpose pretrained_model weights unused (@pakiessling, #90)
  • Prevent spillover during image preprocessing before segmentation (@pakiessling, #90)

Added

  • Blur and CLAHE can be disabled by setting the parameter to 0 (@pakiessling, #90)
  • Added an optional parameter clahe_kernel_size for skimage.exposure.equalize_adapthist (@pakiessling, #90)
  • Check that the image has an integer dtype before segmentation (better error log #92)

[1.1.1] - 2024-07-05

Added

  • Support Xenium multimodal segmentation as a prior for Baysor (#80)
  • For snakemake, you can set a BAYSOR_EXECUTABLE_PATH environment variable to indicate the path of the Baysor executable
  • Added ComSeg segmentation by @tdefa (#76)

Fix

  • Fix Xenium reader issue for recent machine versions (#80)
  • Fix type issue (DataTree and DataArray) related to spatialdata>=0.2.0 (#85)
  • Fix sjoin issue related to geopandas>=1.0.0

Changed

  • Fully depends on spatialdata-io for the MERSCOPE and the Xenium reader
  • Use DataArray and DataTree typing instead of (Multiscale)SpatialImage (as in spatialdata>=0.2.0)

[1.1.0] - 2024-06-11

First post-publication release

Changed

  • Using rioxarray as a default backend for MERSCOPE data if installed
  • Lower RAM usage for channels aggregation
  • Transcript-segmentation API more general (not Baysor-specific)

Fixed

  • Encoding issue while writing the report (#64)

[1.0.14] - 2024-04-25

Changed

  • Renamed embed_wsi_patches to infer_wsi_patches
  • infer_wsi_patches now accepts also callables
  • Improves tile gathering speed and decreases overall computation of tile-wise inference

[1.0.13] - 2024-04-22

Changed

  • Xenium reader now adds channel names, and support more recent versions (#68)
  • Renamed sopa.embedding into sopa.patches, and moved internal files
  • Don't recompute to_multiscale if the right scales are already used for Xenium Explorer image writing

Added

  • New tutorial on Xenium Explorer interoperability

[1.0.12] - 2024-05-17

Fix

  • Fix polygon selection when no channel is provided
  • Fix CosMX reader for proteins
  • Fix FOV column issue for CosMX data (#65)

Added

  • Check the columns of CosMX data to see if the correct export module was used

Changed

  • Ensure categorical variables are used for patches clustering

[1.0.11] - 2024-04-26

Added

  • Can overlay a custom segmentation (merge boundaries)
  • Xenium Explorer selection(s) can be added as shapes in a SpatialData object
  • Optionnal OpenSlide backend for WSI data
  • New sopa.io.aicsimageio reader for special formats (#58)

Changed

  • Rename Aggregator.update_table to Aggregator.compute_table

[1.0.10] - 2024-04-08

Added

  • CosMX reader with image stitching (experimental)

Changed

  • Default min_transcripts set in snakemake configs
  • Minimum number of transcripts per patch set to 4000 (#41)
  • Config files refactoring (configs added or renamed)
  • Readers refactoring
  • Section with error during report are not displayed (instead of throwing an error)

[1.0.9] - 2024-04-03

Added:

  • Support multiple tables

Fixed

  • Spatial elements not saved when data is not backed

[1.0.8] - 2024-04-02

Hotfix: resolve issues related to spatialdata>=1.0.0

[1.0.7] - 2024-03-29

Changed

  • Improvements in the CLI and API tutorials
  • Sequential segmentation now requires patchify to be run independently
  • Dependency spatialdata>=0.1.1

Added

  • Kwargs can be provided to Cellpose model init

Fixed

  • set_transformation issue for image alignment
  • Import issue #37 #39

[1.0.6] - 2024-03-13

Added

  • Spatial join between shapes (from sdata.spatial import sjoin)
  • H&E tutorial (basic usage)
  • New backend for the MERSCOPE reader (requires rioxarray, currently experimental, should use less RAM)

Changed

  • Using MultiscaleSpatialImage by default for multiplex imaging technologies

Fixed

  • Issue in report creation when channel names are integers

[1.0.5] - 2024-03-01

Changed

  • Faster image writing for the Xenium Explorer (about x5 speedup)
  • Cellpose default model set to "cyto3" (new cellpose version)
  • Cell GeoDataFrame index consistent with obs_names

Added

  • Support for python 3.9 to 3.11 (we still recommend python==3.10)
  • Support WSI analysis: reader, tissue segmentation, patch embedding (tutorials coming soon)
  • Supporting multiple region-of-interest queries
  • Can load a custom cellpose model using the pretrained_model/model_type argument

[1.0.4] - 2024-02-14

Fix

  • Missing transcript count in cells due to concurrent writing processes (#20)

Changed

  • Explorer images should have a higher contrast (not clipping values anymore)

[1.0.3] - 2024-02-12

Breaking changes

  • pixelsize argument has been renamed to pixel_size (the snakemake pipeline is only deprecating it for now)

Added

  • The phenocycler reader can now also read .tif files (not just .qptiff)
  • Added missing legend in the HTML report under the "Channels" section (#15)
  • The cell area is also stored in the table (in .obs["area"])

Changed

  • The uniform toy dataset now has two coordinate systems (better test case)
  • Faster table conversion to the Xenium Explorer

Fixed

  • Tight patching more stable with epsilon constant

[1.0.2] - 2024-01-15

Fix

  • When geometries are GeometryCollection, convert them back to Polygons (#11)
  • Give min_area parameter to the right Baysor function in snakemake

Added

  • API tutorial
  • sopa.spatial tutorial
  • Docstrings for the snakemake pipeline utils
  • Show right micron scale in the Xenium Explorer

Changed

  • sopa.stats is now called sopa.spatial

[1.0.1] - 2024-01-10

Added

  • Tutorial on CLI usage
  • Tutorial on image alignment with the Xenium Explorer
  • Multi-step segmentation (#8)
  • Tutorial for multi-step segmentation and custom segmentation
  • Improved installation guide

Fix

  • CLI issue (missing file) when used without Snakemake

Change

  • Use .parquet instead of .zarr.zip format to store intermediate boundary polygons

[1.0.0] - 2023-12-26

Added