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Expand Up @@ -10,140 +10,140 @@ and this project adheres to [Semantic Versioning][].

## incoming release

- (Visium/Visium HD) lowres and hires images now mapped also to the 'global' coordinate system #230
- (Macsima) added support @berombau #224
- (seqFISH) support for v2 instrument #227
- (Visium HD) added argument `annotate_table_by_labels` to rasterize the bins as labels #211 @ArneDefauw
- (Visium/Visium HD) lowres and hires images now mapped also to the 'global' coordinate system #230
- (Macsima) added support @berombau #224
- (seqFISH) support for v2 instrument #227
- (Visium HD) added argument `annotate_table_by_labels` to rasterize the bins as labels #211 @ArneDefauw

## [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
- (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

## [0.1.5] - 2024-09-25

### Added

- (Xenium) added `dims` parameter for more control in `xenium_aligned_image()`
- (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
- 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

## [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
- (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

## [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
- (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.
- (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"
- (MERSCOPE) "global" coordinate system is used as a default instead of "microns"

## [0.1.2] - 2024-03-30

### Added

- (Visium HD) added reader, coauthored by @LLehner
- (Visium HD) added reader, coauthored by @LLehner

### Fixed

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

## [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)
- (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
- (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

## [0.0.9] - 2023-11-06

### Fixed

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

## [0.0.8] - 2023-10-02

### Fixed

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

## [0.0.7] - 2023-07-23

### Fixed

- Bugs in Xenium and MERSCOPE
- Bugs in Xenium and MERSCOPE

## [0.0.5] - 2023-06-21

### Added

- MERFISH reader (from @quentinblampey)
- CODEX reader (from @LLehner)
- MERFISH reader (from @quentinblampey)
- CODEX reader (from @LLehner)

### Fixed

- Issues on Visium reader (thanks @ilia-kats) and Xenium reader
- Issues on Visium reader (thanks @ilia-kats) and Xenium reader

## [0.0.4] - 2023-05-23

### Added

- Curio reader
- Curio reader

## [0.0.3] - 2023-05-22

### Merged

- Merge pull request #40 from scverse/fix/categories
- Merge pull request #40 from scverse/fix/categories

## [0.0.2] - 2023-05-04

### Changed

- Revert version regex (#37)
- Revert version regex (#37)

## [0.0.1] - 2023-05-04

### Tested

- Test installation from pypi
- Test installation from pypi

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