gustaveroussy · quentinblampey · Apr 26, 2024 · Apr 9, 2024 · Apr 9, 2024 · Apr 9, 2024
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,8 +1,12 @@
-## [1.0.11] - 2024-xx-xx
+## [1.x.x] - xxxx-xx-xx
+
+## [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` to `Aggregator.compute_table`

diff --git a/docs/api/_sdata.md b/docs/api/_sdata.md
@@ -2,25 +2,13 @@
     These are convenient tools that operates on `SpatialData` objects
 
 ::: sopa._sdata.get_boundaries
-    options:
-      show_root_heading: true
 
 ::: sopa._sdata.get_intrinsic_cs
-    options:
-      show_root_heading: true
 
 ::: sopa._sdata.to_intrinsic
-    options:
-      show_root_heading: true
 
 ::: sopa._sdata.get_intensities
-    options:
-      show_root_heading: true
 
 ::: sopa._sdata.iter_scales
-    options:
-      show_root_heading: true
 
 ::: sopa._sdata.get_spatial_image
-    options:
-      show_root_heading: true
diff --git a/docs/api/annotation.md b/docs/api/annotation.md
@@ -0,0 +1,5 @@
+::: sopa.annotation.tangram_annotate
+
+::: sopa.annotation.higher_z_score
+
+::: sopa.annotation.preprocess_fluo
diff --git a/docs/api/annotation/fluorescence.md b/docs/api/annotation/fluorescence.md
diff --git a/docs/api/annotation/tangram.md b/docs/api/annotation/tangram.md
diff --git a/docs/api/embedding.md b/docs/api/embedding.md
@@ -1,3 +1 @@
 ::: sopa.embedding.embed_wsi_patches
-    options:
-      show_root_heading: true
diff --git a/docs/api/io.explorer.md b/docs/api/io.explorer.md
diff --git a/docs/api/io.md b/docs/api/io.md
@@ -1,45 +1,51 @@
+# sopa.io
+
 !!! notes
     Due to many updates in the data format provided by the different companies, you might have issues loading your data. In this case, consider [opening an issue](https://github.com/gustaveroussy/sopa/issues) detailing the version of the machine you used and the error log, as well as an example of file names that you are trying to read.
 
 !!! notes "Related to `spatialdata-io`"
     A library called [`spatialdata-io`](https://spatialdata.scverse.org/projects/io/en/latest/) already contains a lot of readers. Here, we updated some readers already existing in `spatialdata-io`, and added a few others. In the future, we will completely rely on `spatialdata-io`.
 
+## Readers
+
 ::: sopa.io.xenium
-    options:
-      show_root_heading: true
 
 ::: sopa.io.merscope
-    options:
-      show_root_heading: true
 
 ::: sopa.io.cosmx
-    options:
-      show_root_heading: true
 
 ::: sopa.io.macsima
-    options:
-      show_root_heading: true
 
 ::: sopa.io.phenocycler
-    options:
-      show_root_heading: true
 
 ::: sopa.io.hyperion
-    options:
-      show_root_heading: true
+
+::: sopa.io.aicsimageio
 
 ::: sopa.io.ome_tif
-    options:
-      show_root_heading: true
 
 ::: sopa.io.wsi
-    options:
-      show_root_heading: true
 
 ::: sopa.io.uniform
-    options:
-      show_root_heading: true
 
 ::: sopa.io.blobs
-    options:
-      show_root_heading: true
+
+## Xenium Explorer
+
+::: sopa.io.write
+
+::: sopa.io.align
+
+::: sopa.io.add_explorer_selection
+
+::: sopa.io.int_cell_id
+
+::: sopa.io.str_cell_id
+
+::: sopa.io.write_image
+
+::: sopa.io.save_column_csv
+
+## Report
+
+::: sopa.io.write_report
diff --git a/docs/api/io.report.md b/docs/api/io.report.md
diff --git a/docs/api/segmentation/aggregate.md b/docs/api/segmentation/aggregate.md
@@ -1,23 +1,11 @@
 ::: sopa.segmentation.aggregate.overlay_segmentation
-    options:
-      show_root_heading: true
 
 ::: sopa.segmentation.aggregate.average_channels
-    options:
-      show_root_heading: true
 
 ::: sopa.segmentation.aggregate._average_channels_aligned
-    options:
-      show_root_heading: true
 
 ::: sopa.segmentation.aggregate.count_transcripts
-    options:
-      show_root_heading: true
 
 ::: sopa.segmentation.aggregate._count_transcripts_aligned
-    options:
-      show_root_heading: true
 
 ::: sopa.segmentation.aggregate.Aggregator
-    options:
-      show_root_heading: true
diff --git a/docs/api/segmentation/baysor.md b/docs/api/segmentation/baysor.md
@@ -1,3 +1 @@
 ::: sopa.segmentation.baysor.resolve.resolve
-    options:
-      show_root_heading: true
diff --git a/docs/api/segmentation/methods.md b/docs/api/segmentation/methods.md
@@ -1,3 +1 @@
 ::: sopa.segmentation.methods.cellpose_patch
-    options:
-      show_root_heading: true
diff --git a/docs/api/segmentation/patching.md b/docs/api/segmentation/patching.md
@@ -1,3 +1 @@
 ::: sopa.segmentation.patching.Patches2D
-    options:
-      show_root_heading: true
diff --git a/docs/api/segmentation/shapes.md b/docs/api/segmentation/shapes.md
@@ -1,11 +1,5 @@
 ::: sopa.segmentation.shapes.solve_conflicts
-    options:
-      show_root_heading: true
 
 ::: sopa.segmentation.shapes.geometrize
-    options:
-      show_root_heading: true
 
 ::: sopa.segmentation.shapes.rasterize
-    options:
-      show_root_heading: true
diff --git a/docs/api/segmentation/stainings.md b/docs/api/segmentation/stainings.md
@@ -1,3 +1 @@
 ::: sopa.segmentation.stainings.StainingSegmentation
-    options:
-      show_root_heading: true
diff --git a/docs/api/segmentation/tissue.md b/docs/api/segmentation/tissue.md
@@ -1,3 +1 @@
 ::: sopa.segmentation.tissue.hsv_otsu
-    options:
-      show_root_heading: true
diff --git a/docs/api/spatial.md b/docs/api/spatial.md
@@ -1,27 +1,13 @@
 ::: sopa.spatial.sjoin
-    options:
-      show_root_heading: true
 
 ::: sopa.spatial.mean_distance
-    options:
-      show_root_heading: true
 
 ::: sopa.spatial.geometrize_niches
-    options:
-      show_root_heading: true
 
 ::: sopa.spatial.niches_geometry_stats
-    options:
-      show_root_heading: true
 
 ::: sopa.spatial.cells_to_groups
-    options:
-      show_root_heading: true
 
 ::: sopa.spatial.spatial_neighbors
-    options:
-      show_root_heading: true
 
 ::: sopa.spatial.prepare_network
-    options:
-      show_root_heading: true
diff --git a/docs/api/utils/image.md b/docs/api/utils/image.md
@@ -1,11 +1,5 @@
 ::: sopa.utils.image.scale_dtype
-    options:
-      show_root_heading: true
 
 ::: sopa.utils.image.resize
-    options:
-      show_root_heading: true
 
 ::: sopa.utils.image.resize_numpy
-    options:
-      show_root_heading: true
diff --git a/docs/api/utils/polygon_crop.md b/docs/api/utils/polygon_crop.md
@@ -1,3 +1 @@
 ::: sopa.utils.polygon_crop.polygon_selection
-    options:
-      show_root_heading: true
diff --git a/docs/tutorials/align.md b/docs/tutorials/align.md
@@ -5,11 +5,10 @@ Convert your image with QuPath as written in this [10x genomics webpage](https:/
 
 If you are not familiar with QuPath, you can also use our API to write the image:
 ```python
-from sopa import io
-from sopa.io.explorer import write_image
+import sopa.io
 
-image = io.ome_tif("path/to/your/image.tif") # or use a different reader
-write_image("where/to/save/image.ome.tif", image, is_dir=False)
+image = sopa.io.ome_tif("path/to/your/image.tif") # or use a different reader
+sopa.io.write_image("where/to/save/image.ome.tif", image, is_dir=False)
 ```
 
 !!! note "Xenium users"

diff --git a/mkdocs.yml b/mkdocs.yml
@@ -31,11 +31,7 @@ nav:
       - sopa.segmentation.tissue: api/segmentation/tissue.md
       - sopa.segmentation.baysor: api/segmentation/baysor.md
     - sopa.io: api/io.md
-    - sopa.io.explorer: api/io.explorer.md
-    - sopa.io.report: api/io.report.md
-    - sopa.annotation:
-      - sopa.annotation.tangram: api/annotation/tangram.md
-      - sopa.annotation.fluorescence: api/annotation/fluorescence.md
+    - sopa.annotation: api/annotation.md
     - sopa.utils:
       - sopa.utils.image: api/utils/image.md
       - sopa.utils.polygon_crop: api/utils/polygon_crop.md
@@ -45,7 +41,12 @@ nav:
   - Cite us: cite_us.md
 plugins:
   - search
-  - mkdocstrings
+  - mkdocstrings:
+      handlers:
+        python:
+          options:
+            show_root_heading: true
+            heading_level: 3
   - mkdocs-jupyter:
       include_source: True
 markdown_extensions:

diff --git a/pyproject.toml b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "sopa"
-version = "1.0.10"
+version = "1.0.11"
 description = "Spatial-omics pipeline and analysis"
 documentation = "https://gustaveroussy.github.io/sopa"
 homepage = "https://gustaveroussy.github.io/sopa"

diff --git a/sopa/annotation/__init__.py b/sopa/annotation/__init__.py
@@ -1 +1,2 @@
 from .fluorescence import preprocess_fluo, higher_z_score
+from .tangram import tangram_annotate