From fbdb22467c38f2052809feacea6d5fdc65cb2f79 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 29 Jun 2026 17:50:58 +0000 Subject: [PATCH 1/2] [pre-commit.ci] pre-commit autoupdate MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/rbubley/mirrors-prettier: v3.8.4 → v3.9.1](https://github.com/rbubley/mirrors-prettier/compare/v3.8.4...v3.9.1) - [github.com/astral-sh/ruff-pre-commit: v0.15.18 → v0.15.20](https://github.com/astral-sh/ruff-pre-commit/compare/v0.15.18...v0.15.20) --- .pre-commit-config.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 27495050..20211bd8 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -9,7 +9,7 @@ ci: skip: [] repos: - repo: https://github.com/rbubley/mirrors-prettier - rev: v3.8.4 + rev: v3.9.1 hooks: - id: prettier exclude: ^.github/workflows/test.yaml @@ -20,7 +20,7 @@ repos: additional_dependencies: [numpy, types-requests] exclude: tests/|docs/ - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.15.18 + rev: v0.15.20 hooks: - id: ruff args: [--fix, --exit-non-zero-on-fix] From 6502f8a7c115d4613411b6408c2436abd8e96f6c Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 29 Jun 2026 17:53:47 +0000 Subject: [PATCH 2/2] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- docs/user_guide.md | 62 ++++++++++++++++++++++------------------------ 1 file changed, 30 insertions(+), 32 deletions(-) diff --git a/docs/user_guide.md b/docs/user_guide.md index efb1a8b8..3f032351 100755 --- a/docs/user_guide.md +++ b/docs/user_guide.md @@ -37,17 +37,17 @@ Please see [this section](https://spatialdata.scverse.org/en/stable/tutorials/no

If you have an existing Squidpy object.

 - + Please have a look at [this tutorial](https://github.com/scverse/spatialdata-notebooks/blob/main/notebooks%2Fexamples%2Fsdata_from_scratch.ipynb). - +
- +

If you want to start from raw files

 - + If you don’t have a SpatialData object or corresponding zarr file, you will have to create a SpatialData object to make use of the SpatialData framework. -You can create a SpatialData object directly from your raw files (e.g. CSVs, cell-gene matrix/cell-proteins matrix, images etc.) by using the [spatialdata-io](https://github.com/scverse/spatialdata-io) library that has reader functions for most spatial omics techniques. See [here](https://spatialdata.scverse.org/projects/io/en/latest/) for a list of currently supported technologies. - +You can create a SpatialData object directly from your raw files (e.g. CSVs, cell-gene matrix/cell-proteins matrix, images etc.) by using the [spatialdata-io](https://github.com/scverse/spatialdata-io) library that has reader functions for most spatial omics techniques. See [here](https://spatialdata.scverse.org/projects/io/en/latest/) for a list of currently supported technologies. + For example, if you have data coming from a MERSCOPE®, just use: ``` @@ -61,12 +61,12 @@ Please also see [this section](https://spatialdata.scverse.org/en/stable/tutoria If there is no reader implemented for your data type, please refer to [this section](https://spatialdata.scverse.org/en/stable/tutorials/notebooks/notebooks/examples/models1.html#construct-a-spatialdata-object-from-scratch) to learn about building SpatialData objects from scratch.
- +

If you want to play around with existing data.

 - + Please see [here](https://spatialdata.scverse.org/en/stable/tutorials/notebooks/datasets/README.html) for a repository of demo datasets (already available as .zarr) generated with different spatial omics technologies. - +
@@ -92,41 +92,40 @@ Yes → Check out our [Transformation/coordinate system tutorial](https://spatia
-

How do I annotate my data?

 - - Annotation can have a lot of meanings. You might want to annotate specific regions in your tissue as tumor, add more details about your cell shapes, group together specific transcripts, include celltype annotations or cell sizes for your cells etc. +

How do I annotate my data?

 + +Annotation can have a lot of meanings. You might want to annotate specific regions in your tissue as tumor, add more details about your cell shapes, group together specific transcripts, include celltype annotations or cell sizes for your cells etc.

How can I spatially annotate regions in my data?

- + This is possible within the SpatialData framework, making use of napari, like explained [in this tutorial](https://spatialdata.scverse.org/en/stable/tutorials/notebooks/notebooks/examples/napari_rois.html).

I have annotated regions in an external tool, how do I add them to SpatialData?

 - -If the annotated regions are saved in a geojson, you can add them as follows: -``` + +If the annotated regions are saved in a geojson, you can add them as follows: + +``` from spatialdata.models import ShapesModel sdata['very_interesting_regions']=ShapesModel.parse('path_to_geojson') ``` + For more details, including information on how to add annotations for these regions, please have a look at [this tutorial](https://spatialdata.scverse.org/en/stable/tutorials/notebooks/notebooks/examples/tables.html).
- +
- - +

I have cells in my dataset, how do I annotate them? (usage of AnnData)

 One of the most obvious things to do for spatial omics data is to annotate cells using the [AnnData](https://anndata.readthedocs.io/en/stable/) format (called tables in SpatialData). These tables can contain count/intensity data, all types of annotations, and make it possible to make use of [scanpy](https://scanpy.readthedocs.io/en/stable/) functionality (normalization/clustering/DE calculation). If you want more technical details on how to create a table from scratch to annotate your shapes/labels/points, you can have a look [here](https://spatialdata.scverse.org/en/stable/tutorials/notebooks/notebooks/examples/models2.html#tables).
- - - +
- +

How do I analyze a spatial subset of my data?

@@ -136,20 +135,19 @@ Therefore, subsampling your data based on spatial coordinates can be helpful. Ot

I want to annotate a specific region myself.

 - + Please see the previous section ('How do I annotate my data?') and then specifically the section about spatially annotating regions. This will guide you through the process of extracting coordinates, which will be used for spatially subsetting the data. Next, see below.

I know the coordinates of the region I want to subsample.

 - + You will need to perform a spatial query, which filters the data based on spatial coordinates. Please see [this tutorial](https://spatialdata.scverse.org/en/stable/tutorials/notebooks/notebooks/examples/spatial_query.html). - +
- - +

How do I visualize my data?

 @@ -191,9 +189,9 @@ The method of aggregation depends on the type of elements in your SpatialData ob
- +

SpatialData looks amazing, I want to learn more. Give me all the technical details!

 - + Sure, no problem! There is much more to learn about SpatialData. You want to learn how to combine SpatialData and deep learning? We got you covered [here](https://spatialdata.scverse.org/en/stable/tutorials/notebooks/notebooks/examples/densenet.html). @@ -203,9 +201,9 @@ If you want to create a labels layer from your shapes (rasterize), a shapes laye Finally here is a more [advanced technical tutorial on transformations](https://spatialdata.scverse.org/en/latest/tutorials/notebooks/notebooks/examples/transformations_advanced.html#other-technical-topics).
- +
- +

I am sold, how can I get in touch and contribute to SpatialData?