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Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[0.5.4] - 2024-11-26

Changed

  • Support for xarray.DataTree (which moved from datatree.DataTree)

Added

  • CLI interface from spatialdata branch
  • New function to get layer by name #315 @minhtien-trinh
  • New annotation function to display text near polygons #315 @minhtien-trinh

Fixed

  • Bug wrong radii transformed circles (e.g. with Visium lowres) #318
  • Bugs: instance id shifted by 1; obsm visualization; background color for labels #320
  • Bug adjusting contrast limit for RGB data #276

[0.5.3] - 2024-09-25

Fixed

  • Bug table was not reset after an element without table was added #317
  • Bug when changing channel for a multichannel image #301 #302
  • Bug when plotting catgorical annotations on points #304

[0.5.2] - 2024-08-16

Minor

  • Modernized release workflow

[0.5.1] - 2024-08-07

Changed

  • RGB is now detected based on axis names in .c (pass ("r","g","b") or ("r","g","b", "a")to c_coords argument when parsing the Image(2D / 3D)Model) @aeisenbarth #153

[0.5.0] - 2024-07-03

Added

  • New annotation widget for managing shapes annotations @melonora #233 #261
  • Showing image channel names in var widget for easy channel selection #254

Fixed

  • Fixed scatterplot widget #247
  • Fixed contrast limits for images #265

[0.4.1] - 2024-03-30

Fixed

  • Saving shapes and points with Shift + E now saves 2D data (a z dim was wrongly added)

[0.4.0] - 2024-03-24

Added

  • Multi table support #199 @melonora
  • Color shapes and points by values in dataframe in addition to tables #216

Fixed

  • Avoid exception when registering shortcuts #201 @aeisenbarth
  • Fix wrong point size when affine specified #193
  • Wrong element visiblity when changing coordinate system #207
  • Cleaned up data model #180
  • Fixes correct matching of geometies and annoations via join #208
  • Better docstrings #219

[0.3.1] - 2023-11-11

Fix

  • removed npe (napari plugin engine) dependency

[0.3.0] - 2023-11-09

Added

  • New APIs for changing coordinate systems #169
  • New APIs for adding single elements #170
  • Improved code to link new layers to layers with a SpatialData object #173

Fixed

  • Enabled saving annotations #168
  • Added safeguard when table is None #177 @aeisenbarth
  • Fix plotting annotations when changing element #175
  • Fixed installation requirements #185 @goanpeca

[0.2.8] - 2023-10-30

Added

  • Global parameters POINT_THRESHOLD and POLYGON_THRESHOLD added to allow users to adjust these parameters.

Fixed

  • Updated dependencies
  • Updated installation instructions since napari conda-forge no longer installs Qt backend. @psobolewskiPhD
  • Allow for viewing SpatialData object with no annotations. @aeisenbarth

[0.2.7] - 2023-10-02

Added

  • Multiple SpatialData objects support (ported from the "spatialdata" branch)
  • Interactive is more ergonomic, has a headless parameter, can be used to display pre-configured elements
  • Remembering user layer visibility settings when changing coordinate system

Fixed

  • Fixes in CLI
  • Several internal bugfixes and code refactorings
  • Fixes in updating affine transformation when changing coordinate system

[0.2.6] - 2023-07-13

Fixed

  • Wrong tag preventing the release to pip (the previous tag was not of a commit merged to main).

[0.2.5] - 2023-07-13

Fixed

  • CLI @berombau @LucaMarconato
  • Display of points and circles @LucaMarconato
  • Issue with name reinitialization @tothmarcella
  • Reverted to use PyQt5 @melonora
  • RGB/RGBA correctly displayed for 3/4 channel images @rahulbshrestha
  • Layer visibility changes when changing coordinate system @melonora
  • Performance with multiscale images @LucaMarconato
  • Refactored internal code to prepare for future refactoring @melonora

Thanks

  • Reviewers @giovp @timtreis @kevinyamauchi and the users that reported bugs.

[0.2.4] - 2023-05-23

Added

  • Color circles and polygons with annotations (#73)

[0.2.3] - 2023-05-11

Fixed

  • Shapes support

[0.2.1] - 2023-05-04

Fixed

  • Package versioning (#63)

[0.2.0] - 2023-05-04

Merged

  • Merge pull request #62 from scverse/kevinyamauchi-patch-1 - Install spatialdata from pypi