Releases: gustaveroussy/sopa
Releases · gustaveroussy/sopa
v1.1.3
[1.1.3] - 2024-08-18
Fix
- Fixed aggregation issue when gene names are
NaN
orNone
(#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
andaicsimageio
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
andDataArray
) related tospatialdata>=0.2.0
(#85) - Fix
sjoin
issue related togeopandas>=1.0.0
Changed
- Fully depends on
spatialdata-io
for the MERSCOPE and the Xenium reader - Use
DataArray
andDataTree
typing instead of (Multiscale)SpatialImage (as inspatialdata>=0.2.0
)
v1.1.0
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
intosopa.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
toAggregator.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)
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)