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)

v1.0.9 (hotfix)

[1.0.9] - 2024-04-02

Hotfix: resolve issues related to spatialdata>=1.0.0 (#37, #43, #5)

v1.0.7

[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 (for instance, to use the GPU)

Fixed

• set_transformation issue for image alignment
• Import issue (#37, #39)