From 9684edbf847be14b749fa5d31c5732fd1c66a87f Mon Sep 17 00:00:00 2001 From: selmanozleyen Date: Wed, 1 Oct 2025 13:53:21 +0200 Subject: [PATCH 1/3] init --- examples/index.rst | 10 ++++++++++ examples/{image => older_versions}/compute_crops.ipynb | 0 2 files changed, 10 insertions(+) rename examples/{image => older_versions}/compute_crops.ipynb (100%) diff --git a/examples/index.rst b/examples/index.rst index 5ac8dda..b0ccc29 100644 --- a/examples/index.rst +++ b/examples/index.rst @@ -65,3 +65,13 @@ This section contains various examples from the :mod:`squidpy.pl` module. :glob: plotting/plot_* + + +Older versions +--------------- +This section contains examples from older versions of Squidpy. Kept here for reference. + +.. toctree:: + :maxdepth: 1 + + older_versions/compute_crops.ipynb \ No newline at end of file diff --git a/examples/image/compute_crops.ipynb b/examples/older_versions/compute_crops.ipynb similarity index 100% rename from examples/image/compute_crops.ipynb rename to examples/older_versions/compute_crops.ipynb From bdd8bfe3fbfa12e432a8098478924c512897a4ae Mon Sep 17 00:00:00 2001 From: selmanozleyen Date: Wed, 1 Oct 2025 15:36:52 +0200 Subject: [PATCH 2/3] update notebooks --- deprecated_features/index.rst | 9 +++++++++ .../tutorial_napari.ipynb | 0 .../compute_crops.ipynb | 17 ----------------- examples/image/compute_custom_features.ipynb | 10 +++++++--- .../image/compute_segmentation_features.ipynb | 14 +++++++++++--- tutorials/index.rst | 2 -- 6 files changed, 27 insertions(+), 25 deletions(-) create mode 100644 deprecated_features/index.rst rename {tutorials => deprecated_features}/tutorial_napari.ipynb (100%) rename examples/{older_versions => image}/compute_crops.ipynb (99%) diff --git a/deprecated_features/index.rst b/deprecated_features/index.rst new file mode 100644 index 0000000..4ffd7f9 --- /dev/null +++ b/deprecated_features/index.rst @@ -0,0 +1,9 @@ +Deprecated Features +========= + +This section contains various deprecated features in :mod:`squidpy`. We keep notebook here that we don't expect to be run by our current suggested workflow. + +.. toctree:: + :maxdepth: 1 + + tutorial_napari diff --git a/tutorials/tutorial_napari.ipynb b/deprecated_features/tutorial_napari.ipynb similarity index 100% rename from tutorials/tutorial_napari.ipynb rename to deprecated_features/tutorial_napari.ipynb diff --git a/examples/older_versions/compute_crops.ipynb b/examples/image/compute_crops.ipynb similarity index 99% rename from examples/older_versions/compute_crops.ipynb rename to examples/image/compute_crops.ipynb index f79f58a..8416e88 100644 --- a/examples/older_versions/compute_crops.ipynb +++ b/examples/image/compute_crops.ipynb @@ -207,23 +207,6 @@ "adata_crop = crop_corner.subset(adata)\n", "adata_crop" ] - }, - { - "attachments": {}, - "cell_type": "markdown", - "metadata": {}, - "source": [ - "Visualize the result in Napari:\n" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "crop_corner.interactive(adata_crop)" - ] } ], "metadata": { diff --git a/examples/image/compute_custom_features.ipynb b/examples/image/compute_custom_features.ipynb index feb2cbe..4aefe93 100644 --- a/examples/image/compute_custom_features.ipynb +++ b/examples/image/compute_custom_features.ipynb @@ -230,11 +230,15 @@ "metadata": {}, "source": [ "Use `squidpy.pl.extract` to plot the histogram features on the tissue\n", - "image or have a look at [our interactive visualization\n", - "tutorial](../../tutorials/tutorial_napari.ipynb) to learn how to use our\n", - "interactive `napari` plugin.\n" + "image or have a look at [napari-spatialdata](https://spatialdata.scverse.org/projects/napari/en/stable/notebooks/spatialdata.html). Here, we show all calculated segmentation\n", + "features.\n" ] }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [] + }, { "cell_type": "code", "execution_count": 8, diff --git a/examples/image/compute_segmentation_features.ipynb b/examples/image/compute_segmentation_features.ipynb index a8ae2f0..36f5cf7 100644 --- a/examples/image/compute_segmentation_features.ipynb +++ b/examples/image/compute_segmentation_features.ipynb @@ -322,12 +322,20 @@ "metadata": {}, "source": [ "Use `squidpy.pl.extract` to plot the texture features on the tissue\n", - "image or have a look at [our interactive visualization\n", - "tutorial](../../tutorials/tutorial_napari.ipynb) to learn how to use our\n", - "interactive `napari` plugin. Here, we show all calculated segmentation\n", + "image or have a look at [napari-spatialdata](https://spatialdata.scverse.org/projects/napari/en/stable/notebooks/spatialdata.html). Here, we show all calculated segmentation\n", "features.\n" ] }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [] + }, { "cell_type": "code", "execution_count": 8, diff --git a/tutorials/index.rst b/tutorials/index.rst index 86748da..3fa8ba9 100644 --- a/tutorials/index.rst +++ b/tutorials/index.rst @@ -28,7 +28,6 @@ Advanced Tutorials This section contains tutorials showcasing advanced :mod:`squidpy` functionalities, such as: - loading spatial data. - - interactive visualization. - working with z-stacks. .. toctree:: @@ -36,7 +35,6 @@ This section contains tutorials showcasing advanced :mod:`squidpy` functionaliti tutorial_read_spatial tutorial_image_container - tutorial_napari tutorial_image_container_zstacks From 98d97da49528e4229548a315a88569ebfc618942 Mon Sep 17 00:00:00 2001 From: selmanozleyen Date: Wed, 1 Oct 2025 15:41:12 +0200 Subject: [PATCH 3/3] remove empty cells --- examples/image/compute_custom_features.ipynb | 5 ----- examples/image/compute_segmentation_features.ipynb | 10 ---------- 2 files changed, 15 deletions(-) diff --git a/examples/image/compute_custom_features.ipynb b/examples/image/compute_custom_features.ipynb index 4aefe93..940e62e 100644 --- a/examples/image/compute_custom_features.ipynb +++ b/examples/image/compute_custom_features.ipynb @@ -234,11 +234,6 @@ "features.\n" ] }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [] - }, { "cell_type": "code", "execution_count": 8, diff --git a/examples/image/compute_segmentation_features.ipynb b/examples/image/compute_segmentation_features.ipynb index 36f5cf7..0e6e9e6 100644 --- a/examples/image/compute_segmentation_features.ipynb +++ b/examples/image/compute_segmentation_features.ipynb @@ -326,16 +326,6 @@ "features.\n" ] }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [] - }, { "cell_type": "code", "execution_count": 8,