release v0.1.4

quentinblampey · quentinblampey · commit 78f98e44373e · 2024-01-11T09:40:02.000+01:00
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -0,0 +1,17 @@
+## [0.1.4] - 2024-01-11
+
+### Fix
+- When a table is sorted or filtered, the polygons are written in the right order (#2)
+
+### Change
+- Now forces using `spatialdata>=0.0.15`
+
+## [0.1.3] - 2023-12-08
+
+### Added
+- New CLI
+- Documentation
+- Support both spatial images and multi-scale spatial images
+- Better memory management during conversion
+- Support image alignment with the explorer
+- Conversion between explorer ID and AnnData ID
diff --git a/README.md b/README.md
@@ -22,6 +22,13 @@ Requirement: `python>=3.9`
 pip install spatialdata_xenium_explorer
 ```
 
+## Features
+
+- Conversion of the following data: images, cell boundaries (polygons), transcripts, cell-by-gene table, and cell categories (or observations).
+- Image alignment can be made on the Xenium Explorer, and then the `SpatialData` object can be updated
+- When working on the `SpatialData` or `AnnData` object, new cell categories can be easily and quickly added to the Explorer
+- When selecting cells with the "lasso tool" on the Explorer, it's easy to select back these cells on the `SpatialData` or `AnnData` object
+
 ## Usage
 
 You can use our CLI or API, see examples below. It will create up to 6 files, among which a file called `experiment.xenium`. Double-click on this file to open it on the [Xenium Explorer](https://www.10xgenomics.com/support/software/xenium-explorer/downloads) (make sure you have the latest version of the software).
diff --git a/docs/cite_us.md b/docs/cite_us.md
@@ -0,0 +1,21 @@
+This library has been detailed in a more general article spatial omics analysis, see the [Sopa library](https://github.com/gustaveroussy/sopa).
+The latter article is not published yet, but you can cite our [preprint](https://www.biorxiv.org/content/10.1101/2023.12.22.571863v1):
+
+```txt
+@article {Blampey2023.12.22.571863,
+	author = {Quentin Blampey & Kevin Mulder et al.},
+	title = {Sopa: a technology-invariant pipeline for analyses of image-based spatial-omics},
+	elocation-id = {2023.12.22.571863},
+	year = {2023},
+	doi = {10.1101/2023.12.22.571863},
+	publisher = {Cold Spring Harbor Laboratory},
+	URL = {https://www.biorxiv.org/content/early/2023/12/23/2023.12.22.571863},
+	eprint = {https://www.biorxiv.org/content/early/2023/12/23/2023.12.22.571863.full.pdf},
+	journal = {bioRxiv}
+}
+```
+
+This library has been developed by Quentin Blampey, PhD student in Biomathematics / Deep Learning. The following institutions funded this work:
+
+- Lab of Mathematics and Computer Science (MICS), **CentraleSupélec** (Engineering School, Paris-Saclay University).
+- PRISM center, **Gustave Roussy Institute** (Cancer campus, Paris-Saclay University).
diff --git a/docs/index.md b/docs/index.md
@@ -2,4 +2,12 @@
 
 Converting any [`SpatialData`](https://github.com/scverse/spatialdata) object into files that can be open by the [Xenium Explorer](https://www.10xgenomics.com/support/software/xenium-explorer).
 
-> *Xenium Explorer* is a registered trademark of 10x Genomics
+> *Xenium Explorer* is a registered trademark of 10x Genomics
+
+You may also be interested in a pipeline for spatial-omics that uses this conversion to Xenium Explorer: see [Sopa](https://github.com/gustaveroussy/sopa).
+
+## Features
+- Conversion of the following data: images, cell boundaries (polygons), transcripts, cell-by-gene table, and cell categories (or observations).
+- Image alignment can be made on the Xenium Explorer, and then the `SpatialData` object can be updated
+- When working on the `SpatialData` or `AnnData` object, new cell categories can be easily and quickly added to the Explorer
+- When selecting cells with the "lasso tool" on the Explorer, it's easy to select back these cells on the `SpatialData` or `AnnData` object
diff --git a/mkdocs.yml b/mkdocs.yml
@@ -1,13 +1,15 @@
 site_name: spatialdata_xenium_explorer
 repo_name: spatialdata_xenium_explorer
+repo_url: https://github.com/quentinblampey/spatialdata_xenium_explorer
 copyright: Copyright &copy; 2023 - 2024 Quentin Blampey
 theme:
   name: material
 nav:
   - Home: index.md
-  - Getting Started: getting_started.md
-  - CLI: cli.md
-  - API: api.md
+  - Getting Started: getting_started
+  - CLI: cli
+  - API: api
+  - Cite us: cite_us
 plugins:
   - search
   - mkdocstrings
diff --git a/poetry.lock b/poetry.lock
diff --git a/pyproject.toml b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "spatialdata_xenium_explorer"
-version = "0.1.3"
+version = "0.1.4"
 description = "Converting any SpatialData object into files that can be open by the Xenium Explorer"
 documentation = "https://quentinblampey.github.io/spatialdata_xenium_explorer/"
 homepage = "https://quentinblampey.github.io/spatialdata_xenium_explorer/"
@@ -24,7 +24,7 @@ spatialdata_xenium_explorer = "spatialdata_xenium_explorer.main:app"
 [tool.poetry.dependencies]
 python = ">=3.9,<3.11"
 botocore = "^1.31.47"
-spatialdata = "^0.0.12"
+spatialdata = "^0.0.15"
 typer = "^0.9.0"
 
 [tool.poetry.group.dev.dependencies]
diff --git a/spatialdata_xenium_explorer/cli/app.py b/spatialdata_xenium_explorer/cli/app.py
@@ -111,7 +111,7 @@ def add_aligned(
     ),
     original_image_key: str = typer.Option(
         None,
-        help="Optional original-image key on which the new image will be aligned. This doesn't need to be provided if there is only one image",
+        help="Optional original-image key (of sdata.images) on which the new image will be aligned. This doesn't need to be provided if there is only one image",
     ),
     overwrite: bool = typer.Option(False, help="Whether to overwrite the image if existing"),
 ):
