v0.6.0

What's Changed

Added

• Add macsima ci datasets by @LucaMarconato in #356
• Parse entire macsima metadata from OME metadata by @MSHelm in #349
• Chunkwise image loader by @lucas-diedrich in #279

Changed

• Load Xenium mask labels using Dask by @marcovarrone in #337
• Modify from_legacy_anndata so that it can read older ST datasets by @timtreis in #347

Fixed

• Use pyarrow 21 in tests to fix xenium bug by @LucaMarconato in #351
• Better dataset_id inference and minor fullres image fix by @quentinblampey in #352
• fix warning visium hd when default value was set by @LucaMarconato in #353
• fix steinbock by @LucaMarconato in #354
• Fixes seqfish reader v2 by @LucaMarconato in #268
• Xenium Reader cleaner way to parse polygons by @timtreis in #283
• Update legacy_anndata.py by @Liripo in #320

New Contributors

• @marcovarrone made their first contribution in #337
• @timtreis made their first contribution in #347
• @Liripo made their first contribution in #320
• @MSHelm made their first contribution in #349
• @lucas-diedrich made their first contribution in #279

Full Changelog: v0.5.1...v0.6.0

v0.5.1

What's Changed

Fixed

• Fix scalefactors error visium hd 3.x by @LucaMarconato in #343

Full Changelog: v0.5.0...v0.5.1

v0.5.0

What's Changed

Added

• Feat: Support for Visium HD cell segmentation in Space Ranger 4.0 by @stephenwilliams22 in #328

New Contributors

• @stephenwilliams22 made their first contribution in #328

Full Changelog: v0.4.0...v0.5.0

v0.4.0

What's Changed

Added

• Contribution guide by @LucaMarconato in #315
• add Xenium 4.0.0 test dataset by @pryvkin10x in #326
• add more xenium 4.0 test datasets by @pryvkin10x in #330
• add support for xenium software 4.0 by @pryvkin10x in #312
• Add visium hd test datasets by @LucaMarconato in #336

Changed

• Use global_z in the merscope coordinates by @quentinblampey in #332

Fixed

• update for zarrv3 branch by @melonora in #324
• fix zarr.open (v3) lacks context manager by @LucaMarconato in #327
• Fix table parameter visium reader by @LucaMarconato in #341

New Contributors

• @pryvkin10x made their first contribution in #326

Full Changelog: v0.3.0...v0.4.0

v0.3.0

What's Changed

Fixed

• Don't share the image_kwargs for dask and imageio by @quentinblampey in #294
• Fix steinbock missing var column by @LucaMarconato in #307
• Fix IO warning by @Zethson in #296
• Xenium conversion of indexes to str by @LucaMarconato in #314

New Contributors

• @Zethson made their first contribution in #296

Full Changelog: v0.2.0...v0.3.0

v0.2.0

What's Changed

Added

• resolves spatialdata_io.xenium() capability to read in xeniumranger v3.0.1.1 resegemented data by @Pancreas-Pratik in #244

Changed

• Rename coordinate systems in visium by @grst in #266
• Include dataset id in visium HD reader by @grst in #278

Fixed

• Fix visium_hd for empty dataset_id (default spaceranger output). by @ddiez in #264
• Avoid base exception type error in cosmx reader by @easlinger in #275
• Cleanup Xenium and CosMx readers by @LucaMarconato in #276
• Visium HD fix bug projective transformation (CytAssist image) by @LucaMarconato in #247
• Small fixes generic reader and cli by @LucaMarconato in #297
• Fix read_generic_wrapper test by @melonora in #301
• fix visium hd wrong global coordinate system by @LucaMarconato in #303

New Contributors

• @ddiez made their first contribution in #264
• @easlinger made their first contribution in #275
• @Pancreas-Pratik made their first contribution in #244

Full Changelog: v0.1.7...v0.2.0

v0.1.7

What's Changed

Major

• MACSima: add reader by @berombau in #224
• Add CLI for spatialdata_io. by @migueLib in #239

Minor

• new test datasets by @LucaMarconato in #248
• Visium HD: represent bins as labels by @ArneDefauw in #211
• Xenium: update xenium.py, fix problem with hidden files in morphology_foucs directory by @psl-schaefer in #260
• Visium HD: handle IF images by @quentinblampey in #261

Changed

• seqFISH: update seqfish reader by @LLehner in #227

Fixed

• VisiumHD: detect full-res image when path is relative by @quentinblampey in #230
• MERSCOPE: reader remove invalid polygons by @ckmah in #207
• Steinbock: fix naming constraints by @LucaMarconato in #265

New Contributors

• @berombau made their first contribution in #224
• @ArneDefauw made their first contribution in #211
• @ckmah made their first contribution in #207
• @migueLib made their first contribution in #239
• @psl-schaefer made their first contribution in #260

Full Changelog: v0.1.6...v0.1.7

v0.1.6

[0.1.6] - 2024-11-26

• (MERSCOPE) added feature_key attribute for points (i.e., the 'gene' column) #210
• (Visium HD) get transformation matrices even when only images are parsed #215
• Support for xarray.DataTree (which was moved from datatree.DataTree) #232

v0.1.5

[0.1.5] - 2024-09-25

Added

• (Xenium) added dims parameter for more control in xenium_aligned_image()

Fixed

• Passing rgb=None to image model parser for both visium and visiumhd, leading to 3-4 channel images being
  interpreted as RGB(A)
• Fix header bug Visium data #200
• (Visium HD) Fix path parsing when images are missing #204 #206

v0.1.4

[0.1.4] - 2024-08-07

Changed

• (Xenium) changed default target of table to labels; radii of circles computed from cells, not nuclei #179
• (Visium HD) changed default geometry to squares from circles for the bins; added parameter to choose #183
• (CosMx) dropping points element with zero-length from the cosmx reader #191