Update

Author: keller-mark

.gitignore

@@ -5,4 +5,5 @@ _build/
 .DS_Store
 notebooks/data
 references/
-Untitled.ipynb
+Untitled.ipynb
+.venv/

README.md

@@ -10,6 +10,14 @@ An overview of the content can be found at [notebooks/Index.ipynb](notebooks/Ind
 
 If you have a Google/Gmail account, you can Run this tutorial from your browser using Colab: [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/vitessce/vitessce-python-tutorial-2026/blob/main/notebooks/Index.ipynb).
 
+### Molab
+
+If colab is not working, you can try Molab instead:
+- [01-Single-Spatial-View.ipynb](https://molab.marimo.io/github/vitessce/vitessce-python-tutorial-2026/blob/main/notebooks/01-Single-Spatial-View.ipynb)
+- [02-Multiple-Views.ipynb](https://molab.marimo.io/github/vitessce/vitessce-python-tutorial-2026/blob/main/notebooks/02-Multiple-Views.ipynb)
+- [03-Available-View-Types.ipynb](https://molab.marimo.io/github/vitessce/vitessce-python-tutorial-2026/blob/main/notebooks/03-Available-View-Types.ipynb)
+- [04-Coordinated-Multiple-Views.ipynb](https://molab.marimo.io/github/vitessce/vitessce-python-tutorial-2026/blob/main/notebooks/04-Coordinated-Multiple-Views.ipynb)
+
 ## Additional materials
 
 Prior tutorial materials can be found in https://github.com/vitessce/vitessce-python-tutorial-2023.
@@ -19,3 +27,55 @@ Prior tutorial materials can be found in https://github.com/vitessce/vitessce-py
 
 The format and structure of these tutorial materials are inspired heavily by the [Gosling Tutorial](https://github.com/gosling-lang/gosling-tutorial) created by Sehi L'Yi, Trevor Manz, Qianwen Wang, and Nils Gehlenborg.
 
+## Local usage
+
+To use these notebooks locally, clone the repository:
+
+```sh
+git clone https://github.com/vitessce/vitessce-python-tutorial-2026.git
+cd vitessce-python-tutorial-2026
+```
+
+We recommend using [uv](https://docs.astral.sh/uv/#installation).
+
+Create the virtual environment:
+
+```sh
+uv venv --python 3.12
+```
+
+Activate the virtual environment:
+
+```sh
+source .venv/bin/activate
+```
+
+Install:
+
+```sh
+uv add --requirements requirements.txt
+```
+
+Run the notebooks
+
+```sh
+uv run jupyter lab
+```
+
+When running the notebooks locally, ignore (i.e., do not run) the `!pip install` lines in the notebooks. Your virtual environment already contains these packages since they are listed in `requirements.txt`.
+
+## Troubleshooting
+
+If you see an anndata error that mentions `allow_write_nullable_strings`, run the following code:
+
+```py
+import anndata
+anndata.settings.allow_write_nullable_strings = True
+```
+
+If you see errors related to missing data, try renaming the output file path and re-running the data writing code:
+
+```diff
+- zarr_path = join("data", "pbmc68k.adata.zarr")
++ zarr_path = join("data", "pbmc68k_v2.adata.zarr")
+```

pyproject.toml

@@ -5,9 +5,10 @@ description = "Add your description here"
 readme = "README.md"
 requires-python = ">=3.12"
 dependencies = [
-    "jupyterlab>=4.5.8",
+    "jupyterlab>=3.0.0",
     "vitessce[all]==3.9.2",
     "spatialdata==0.7.3",
     "spatialdata-plot==0.4.0",
-    "easy_vitessce==0.0.12"
+    "easy-vitessce==0.0.12",
+    "scanpy>=1.12.1",
 ]

requirements.txt

@@ -1,3 +1,6 @@
-jupyter-book==0.13.0
-pandas
+jupyterlab>=3.0.0
 vitessce[all]==3.9.2
+scanpy
+easy-vitessce==0.0.12
+spatialdata==0.7.3
+spatialdata-plot==0.4.0