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

v0.1.3post0

Fix requirement.

v0.1.3

[0.1.3] - 2024-07-03

Added

• (Xenium) support reading multi-polygon selection files from the Xenium Explorer
• (ISS) An experimental loader to load elemental ISS data objects, e.g. raw.tif, label.tif and anndata.h5ad
• (Stereo-seq) Added reader @LLehner @timtreis @florianingelfinger #70
• (MERSCOPE) Optional rioxarray backend for MERSCOPE data (reads chunks)
• (MERSCOPE) Can choose which elements should be loaded

Fixed

• (Visium) Fixed issue with joining a SpatialElement with a table due to index values not being unique.
  obs_names_make_unique is now called internally to enforce unique index values allowing for join operations.

Changed

• (MERSCOPE) "global" coordinate system is used as a default instead of "microns"

v0.1.2

[0.1.2] - 2024-03-30

Added

• (Visium HD) added reader, coauthored with @LLehner

Fixed

• (Xenium) reader for 1.0.1 (paper data) and unknown versions
• (Xenium) fix in reading "minimalistic" Xenium datasets #132

v0.1.1

[0.1.1] - 2024-03-24

Added

• (Xenium) support for post-xenium aligned images (IF, HE)
• (Xenium) reader for the selection coordinates file from the Xenium Explorer
• (Xenium) support for the new Xenium 2.0.0 (multimodal segmentation)
• (Xenium) reading multiscale labels from cells.zarr.zip
• (MCMICRO) support for TMAs (such as the data of exemplar-002)
• (DBiT-seq) reader
• converter functions experimental.to_legacy_anndata() and experimental.from_legacy_anndata()
• (Visium) support for raw reads (capture locations not under tissue)

Fixed

• (Xenium) fixed index (fail on write)
• (Xenium) renamed cells_as_shapes to cells_as_circles; set default to True
• (MERSCOPE) don't try to load unexisting elements #87
• (Visium) fixed axes ordering

v0.1.0-rc0

[0.1.0] - 2024-03-24

Added

• (MCMICRO) support for TMAs (such as the data of exemplar-002)
• (Xenium) support for post-xenium aligned images (IF, HE)
• (Xenium) reader for the selection coordinates file from the Xenium Explorer
• (DBiT-seq) reader
• converter functions experimental.to_legacy_anndata() and experimental.from_legacy_anndata()
• (Visium) support for raw reads (capture locations not under tissue)

Fixed

• (MERSCOPE) don't try to load unexisting elements #87
• (Visium) fixed axes ordering
• (Xenium) fixed index (fail on write)
• (Xenium) renamed cells_as_shapes to cells_as_circles; set default to True

v0.0.9

Fixed

• (Xenium) bug when converting feature_name #81, from @fbnrst
• (Visium) visium() supports file counts without dataset_id #91

v0.0.8

Fixed

• (Xenium) coerce cell id to str #64
• (MERSCOPE) fix coordinate transformation #68
• (MERSCOPE) Improvements/fixes: merscope reader #73