diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 9775c3b..c059ebc 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -14,11 +14,11 @@ repos:
           - id: nbqa-black
           - id: nbqa-isort
     - repo: https://github.com/psf/black
-      rev: 23.7.0
+      rev: 23.9.1
       hooks:
           - id: black
     - repo: https://github.com/pre-commit/mirrors-prettier
-      rev: v3.0.2
+      rev: v3.0.3
       hooks:
           - id: prettier
     - repo: https://github.com/asottile/blacken-docs
@@ -51,7 +51,7 @@ repos:
           - id: trailing-whitespace
           - id: check-case-conflict
     - repo: https://github.com/PyCQA/autoflake
-      rev: v2.2.0
+      rev: v2.2.1
       hooks:
           - id: autoflake
             args:
@@ -71,7 +71,7 @@ repos:
                 - flake8-bugbear
                 - flake8-blind-except
     - repo: https://github.com/asottile/pyupgrade
-      rev: v3.10.1
+      rev: v3.13.0
       hooks:
           - id: pyupgrade
             args: [--py3-plus, --py38-plus, --keep-runtime-typing]
diff --git a/datasets/README.md b/datasets/README.md
index 0f5af25..ae3da53 100644
--- a/datasets/README.md
+++ b/datasets/README.md
@@ -4,19 +4,19 @@ The example notebooks operate on a set of spatial omics datasets that can be dow
 
 Here you can find the dataset hosted in S3 object storage.
 
-|                                                                              Dataset                                                                               |                                      .zarr.zip                                       |                                 S3 (see note below!)                                  |
-| :----------------------------------------------------------------------------------------------------------------------------------------------------------------: | :----------------------------------------------------------------------------------: | :-----------------------------------------------------------------------------------: |
-|                                                                              cosmx_io                                                                              |          <https://s3.embl.de/spatialdata/spatialdata-sandbox/cosmx_io.zip>           |          <https://s3.embl.de/spatialdata/spatialdata-sandbox/cosmx_io.zarr>           |
-|                                                                             mcmicro_io                                                                             |         <https://s3.embl.de/spatialdata/spatialdata-sandbox/mcmicro_io.zip>          |         <https://s3.embl.de/spatialdata/spatialdata-sandbox/mcmicro_io.zarr>          |
-|                                                                              merfish                                                                               |           <https://s3.embl.de/spatialdata/spatialdata-sandbox/merfish.zip>           |           <https://s3.embl.de/spatialdata/spatialdata-sandbox/merfish.zarr>           |
-|                                                                              mibitof                                                                               |           <https://s3.embl.de/spatialdata/spatialdata-sandbox/mibitof.zip>           |           <https://s3.embl.de/spatialdata/spatialdata-sandbox/mibitof.zarr>           |
-|                                                                            steinbock_io                                                                            |        <https://s3.embl.de/spatialdata/spatialdata-sandbox/steinbock_io.zip>         |        <https://s3.embl.de/spatialdata/spatialdata-sandbox/steinbock_io.zarr>         |
-|                                                                                toy                                                                                 |             <https://s3.embl.de/spatialdata/spatialdata-sandbox/toy.zip>             |             <https://s3.embl.de/spatialdata/spatialdata-sandbox/toy.zarr>             |
-|                                                                               visium                                                                               |           <https://s3.embl.de/spatialdata/spatialdata-sandbox/visium.zip>            |           <https://s3.embl.de/spatialdata/spatialdata-sandbox/visium.zarr>            |
-|                                                                             visium_io                                                                              |          <https://s3.embl.de/spatialdata/spatialdata-sandbox/visium_io.zip>          |          <https://s3.embl.de/spatialdata/spatialdata-sandbox/visium_io.zarr>          |
-|                                                                    visium_associated_xenium_io                                                                     | <https://s3.embl.de/spatialdata/spatialdata-sandbox/visium_associated_xenium_io.zip> | <https://s3.embl.de/spatialdata/spatialdata-sandbox/visium_associated_xenium_io.zarr> |
-|                                                                           xenium_rep1_io                                                                           |       <https://s3.embl.de/spatialdata/spatialdata-sandbox/xenium_rep1_io.zip>        |       <https://s3.embl.de/spatialdata/spatialdata-sandbox/xenium_rep1_io.zarr>        |
-|                                                                           xenium_rep2_io                                                                           |       <https://s3.embl.de/spatialdata/spatialdata-sandbox/xenium_rep2_io.zip>        |       <https://s3.embl.de/spatialdata/spatialdata-sandbox/xenium_rep2_io.zarr>        |
+|                                                                         Dataset                                                                          |                                      .zarr.zip                                       |                                 S3 (see note below!)                                  |
+| :------------------------------------------------------------------------------------------------------------------------------------------------------: | :----------------------------------------------------------------------------------: | :-----------------------------------------------------------------------------------: |
+|                                                                         cosmx_io                                                                         |          <https://s3.embl.de/spatialdata/spatialdata-sandbox/cosmx_io.zip>           |          <https://s3.embl.de/spatialdata/spatialdata-sandbox/cosmx_io.zarr>           |
+|                                                                        mcmicro_io                                                                        |         <https://s3.embl.de/spatialdata/spatialdata-sandbox/mcmicro_io.zip>          |         <https://s3.embl.de/spatialdata/spatialdata-sandbox/mcmicro_io.zarr>          |
+|                                                                         merfish                                                                          |           <https://s3.embl.de/spatialdata/spatialdata-sandbox/merfish.zip>           |           <https://s3.embl.de/spatialdata/spatialdata-sandbox/merfish.zarr>           |
+|                                                                         mibitof                                                                          |           <https://s3.embl.de/spatialdata/spatialdata-sandbox/mibitof.zip>           |           <https://s3.embl.de/spatialdata/spatialdata-sandbox/mibitof.zarr>           |
+|                                                                       steinbock_io                                                                       |        <https://s3.embl.de/spatialdata/spatialdata-sandbox/steinbock_io.zip>         |        <https://s3.embl.de/spatialdata/spatialdata-sandbox/steinbock_io.zarr>         |
+|                                                                           toy                                                                            |             <https://s3.embl.de/spatialdata/spatialdata-sandbox/toy.zip>             |             <https://s3.embl.de/spatialdata/spatialdata-sandbox/toy.zarr>             |
+|                                                                          visium                                                                          |           <https://s3.embl.de/spatialdata/spatialdata-sandbox/visium.zip>            |           <https://s3.embl.de/spatialdata/spatialdata-sandbox/visium.zarr>            |
+|                                                                        visium_io                                                                         |          <https://s3.embl.de/spatialdata/spatialdata-sandbox/visium_io.zip>          |          <https://s3.embl.de/spatialdata/spatialdata-sandbox/visium_io.zarr>          |
+|                                                               visium_associated_xenium_io                                                                | <https://s3.embl.de/spatialdata/spatialdata-sandbox/visium_associated_xenium_io.zip> | <https://s3.embl.de/spatialdata/spatialdata-sandbox/visium_associated_xenium_io.zarr> |
+|                                                                      xenium_rep1_io                                                                      |       <https://s3.embl.de/spatialdata/spatialdata-sandbox/xenium_rep1_io.zip>        |       <https://s3.embl.de/spatialdata/spatialdata-sandbox/xenium_rep1_io.zarr>        |
+|                                                                      xenium_rep2_io                                                                      |       <https://s3.embl.de/spatialdata/spatialdata-sandbox/xenium_rep2_io.zip>        |       <https://s3.embl.de/spatialdata/spatialdata-sandbox/xenium_rep2_io.zarr>        |
 | [additional resources for methods developers](https://github.com/scverse/spatialdata-notebooks/blob/main/notebooks/developers_resources/storage_format/) |                                          -                                           |                                           -                                           |
 
 ## Note