Merge branch 'main' into visium/raw_matrix

quentinblampey · Mar 8, 2024 · d9bc12e · d9bc12e
2 parents 1fdebdd + 6fff710
commit d9bc12e
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diff --git a/.gitignore b/.gitignore
@@ -23,6 +23,7 @@ __pycache__/
 # IDEs
 /.idea/
 /.vscode/
+/.spyproject/
 
 # docs
 /docs/generated/

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -7,7 +7,7 @@ default_stages:
 minimum_pre_commit_version: 2.16.0
 repos:
     - repo: https://github.com/psf/black
-      rev: 24.1.1
+      rev: 24.2.0
       hooks:
           - id: black
     - repo: https://github.com/pre-commit/mirrors-prettier
@@ -50,7 +50,7 @@ repos:
           - id: trailing-whitespace
           - id: check-case-conflict
     - repo: https://github.com/PyCQA/autoflake
-      rev: v2.2.1
+      rev: v2.3.0
       hooks:
           - id: autoflake
             args:
@@ -70,7 +70,7 @@ repos:
                 - flake8-bugbear
                 - flake8-blind-except
     - repo: https://github.com/asottile/pyupgrade
-      rev: v3.15.0
+      rev: v3.15.1
       hooks:
           - id: pyupgrade
             args: [--py3-plus, --py39-plus, --keep-runtime-typing]

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -14,6 +14,8 @@ and this project adheres to [Semantic Versioning][].
 
 -   (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
 -   (Visium) support for raw reads (capture locations not under tissue)
 
 ### Fixed

diff --git a/README.md b/README.md
@@ -20,6 +20,7 @@ This package contains reader functions to load common spatial omics formats into
 -   Curio Seeker
 -   Akoya PhenoCycler (formerly CODEX)
 -   Vizgen MERSCOPE (MERFISH)
+-   DBiT-seq
 
 ## Getting started
 
@@ -51,6 +52,15 @@ pip install git+https://github.com/scverse/spatialdata-io.git@main
 For questions and help requests, you can reach out in the [scverse discourse][scverse-discourse].
 If you found a bug, please use the [issue tracker][issue-tracker].
 
+## Readers from third-party libraries
+
+Technologies that can be read into `SpatialData` objects using third-party libraries:
+
+-   METASPACE (MALDI, ...): [metaspace-converter](https://github.com/metaspace2020/metaspace-converter)
+-   PhenoCycler: [SOPA](https://github.com/gustaveroussy/sopa)
+-   MACSima: [SOPA](https://github.com/gustaveroussy/sopa)
+-   Hyperion (Imaging Mass Cytometry): [SOPA](https://github.com/gustaveroussy/sopa)
+
 ## Citation
 
 [L Marconato*, G Palla*, KA Yamauchi*, I Virshup*, E Heidari, T Treis, M Toth, R Shrestha, H Vöhringer, W Huber, M Gerstung, J Moore, FJ Theis, O Stegle, bioRxiv, 2023](https://www.biorxiv.org/content/10.1101/2023.05.05.539647v1). \* = equal contribution

diff --git a/docs/api.md b/docs/api.md
@@ -8,6 +8,8 @@
 
 I/O for the `spatialdata` project.
 
+### Readers
+
 ```{eval-rst}
 .. autosummary::
     :toctree: generated
@@ -20,4 +22,15 @@ I/O for the `spatialdata` project.
     steinbock
     merscope
     mcmicro
+    dbit
+```
+
+### Utility functions
+
+```{eval-rst}
+.. autosummary::
+    :toctree: generated
+
+    xenium_aligned_image
+    xenium_explorer_selection
 ```
diff --git a/docs/conf.py b/docs/conf.py
@@ -94,6 +94,7 @@
     "geopandas": ("https://geopandas.org/en/stable/", None),
     "xarray": ("https://docs.xarray.dev/en/stable/", None),
     "datatree": ("https://datatree.readthedocs.io/en/latest/", None),
+    "shapely": ("https://shapely.readthedocs.io/en/stable/", None),
 }
 
 # List of patterns, relative to source directory, that match files and

diff --git a/src/spatialdata_io/__init__.py b/src/spatialdata_io/__init__.py
@@ -3,11 +3,16 @@
 from spatialdata_io.readers.codex import codex
 from spatialdata_io.readers.cosmx import cosmx
 from spatialdata_io.readers.curio import curio
+from spatialdata_io.readers.dbit import dbit
 from spatialdata_io.readers.mcmicro import mcmicro
 from spatialdata_io.readers.merscope import merscope
 from spatialdata_io.readers.steinbock import steinbock
 from spatialdata_io.readers.visium import visium
-from spatialdata_io.readers.xenium import xenium
+from spatialdata_io.readers.xenium import (
+    xenium,
+    xenium_aligned_image,
+    xenium_explorer_selection,
+)
 
 __all__ = [
     "curio",
@@ -18,6 +23,9 @@
     "mcmicro",
     "steinbock",
     "merscope",
+    "xenium_aligned_image",
+    "xenium_explorer_selection",
+    "dbit",
 ]
 
 __version__ = version("spatialdata-io")
diff --git a/src/spatialdata_io/_constants/_constants.py b/src/spatialdata_io/_constants/_constants.py
@@ -198,3 +198,15 @@ class MerscopeKeys(ModeEnum):
     GLOBAL_Z = "global_z"
     Z_INDEX = "ZIndex"
     REGION_KEY = "cells_region"
+
+
+@unique
+class DbitKeys(ModeEnum):
+    """Keys for DBiT formatted dataset."""
+
+    # files and directories
+    COUNTS_FILE = ".h5ad"
+    # barcodes_file
+    BARCODE_POSITION = "barcode_list"
+    # image
+    IMAGE_LOWRES_FILE = "tissue_lowres_image.png"