diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 2a39f5b..6c9cfca 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -39,12 +39,12 @@ repos: - id: yamllint exclude: pre-commit-config.yaml - repo: https://github.com/astral-sh/ruff-pre-commit - rev: "v0.14.8" + rev: "v0.14.10" hooks: - id: ruff-format - id: ruff-check - repo: https://github.com/rhysd/actionlint - rev: v1.7.9 + rev: v1.7.10 hooks: - id: actionlint - repo: https://gitlab.com/vojko.pribudic.foss/pre-commit-update diff --git a/CITATION.cff b/CITATION.cff index 147b9da..daea164 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -129,3 +129,29 @@ references: JUMP (cpg0000-jump-pilot) was used to help demonstrate CytoDataFrame performance with large data. See here for more information: https://github.com/broadinstitute/cellpainting-gallery + - type: article + authors: + - family-names: Blin + given-names: Guillaume + - family-names: Sadurska + given-names: Dominika + - family-names: Portero Migueles + given-names: Rafael + - family-names: Chen + given-names: Ni + - family-names: Watson + given-names: James A. + - family-names: Lowell + given-names: Sally + title: "Nessys: A new set of tools for the automated detection of nuclei within intact tissues and dense 3D cultures" + journal: PLoS Biology + volume: "17" + issue: "8" + pages: e3000388 + year: 2019 + doi: "10.1371/journal.pbio.3000388" + url: "https://doi.org/10.1371/journal.pbio.3000388" + notes: > + This work used the file "6001240_labels.zarr" from the DISCEPTS imaging + dataset, available through the Image Data Resource (IDR) under accession + number idr0062. diff --git a/docs/src/examples/learning_to_fly_with_ome-arrow.ipynb b/docs/src/examples/learning_to_fly_with_ome-arrow.ipynb index 2dce2d3..f1ff777 100644 --- a/docs/src/examples/learning_to_fly_with_ome-arrow.ipynb +++ b/docs/src/examples/learning_to_fly_with_ome-arrow.ipynb @@ -34,7 +34,7 @@ "2D image, single-channel - shape (T=1, C=1, Z=1, Y=512, X=512)" ], "text/plain": [ - "" + "" ] }, "execution_count": 2, @@ -129,7 +129,7 @@ "3D image (z-stack), multi-channel (2 channels) - shape (T=1, C=2, Z=22, Y=128, X=128)" ], "text/plain": [ - "" + "" ] }, "execution_count": 5, @@ -160,19 +160,19 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": null, "id": "383e1f10-b32f-47cb-9906-15dd9947b09a", "metadata": {}, "outputs": [ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "e438f2316a4b4348b00283242d346c63", + "model_id": "ee038f8ceae842e5b6190bcf038c1318", "version_major": 2, "version_minor": 0 }, "text/plain": [ - "Widget(value='