v2.0.0

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• API: The Aggregator class has been replaced by a simple function wrapper: sopa.aggregate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

v1.1.5

[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

v1.1.3

[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)

v1.1.2

[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)

v1.1.1

[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)

v1.1.0

[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)

v1.0.13

[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

v1.0.12

[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

v1.0.11

[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

v1.0.10

[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)