Add Napari

Dockerfile

@@ -79,3 +79,28 @@ COPY --chown=1000:100 *.desktop /home/jovyan/Desktop/
 
 WORKDIR ${HOME}
 
+# https://github.com/napari/napari/blob/v0.2.2/requirements/default.txt
+RUN conda install --freeze-installed -y -q -c conda-forge \
+    dask \
+    zarr \
+    fsspec \
+    imageio \
+    qtpy \
+    qtconsole \
+    scipy \
+    scikit-image \
+    vispy \
+    backcall \
+    pyopengl \
+    pyside2 \
+    wrapt \
+    numpydoc
+# Already installed:
+    # ipykernel
+    # numpy
+    # ipython
+
+# The conda pyside package doesn't appear in pip list so napari tries to reinstall it
+RUN pip install --no-dependencies napari==0.2.2
+
+COPY napari.ipynb /home/jovyan/

README.md

@@ -1,7 +1,8 @@
 # Jupyter OMERO client Desktop
-[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/manics/jupyter-omeroanalysis-desktop/master?urlpath=Desktop)
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/manics/jupyter-omeroanalysis-desktop/napari?filepath=napari.ipynb)
 
-Run OMERO clients in a Linux desktop using Jupyter.
+
+Run [OMERO clients](https://www.openmicroscopy.org/omero/downloads/) and [Napari](http://napari.org/) in a Linux desktop using Jupyter.
 
 This is based on https://github.com/ryanlovett/nbnovnc
 
@@ -11,3 +12,5 @@ docker run -it --rm -p 8888:8888 jupyter-omeroanalysis-desktop
 ```
 
 Open the displayed URL, then go to `/Desktop` e.g. http://localhost:8888/Desktop and if you're lucky you'll see a Linux desktop with icons for OMERO.insight and FIJI.
+
+Once the desktop is open go back to the main Jupyter Notebook window, open `napari.ipynb` and execute the cells one at a time. You should see Napari open in the Desktop window.

napari.ipynb

@@ -0,0 +1,66 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Napari\n",
+    "\n",
+    "\n",
+    "## Setup: start the [Desktop](../Desktop)\n",
+    "The link should open in a different window. If you see an error message try refreshing the window.\n",
+    "\n",
+    "Then run the first cell and wait for QT to be initialised before running the following cells. `Run all cells` will not work.\n",
+    "\n",
+    "If you are running this locally you should see some log messages. If you are running this on mybinder wait a few seconds before running the Napari cell. Note adding `time.sleep(5)` to the cell does not work!"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Use the novnc Desktop in the other window\n",
+    "import os\n",
+    "os.environ['DISPLAY'] = ':1.0'\n",
+    "# instantiate Qt GUI\n",
+    "%gui qt5"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import napari\n",
+    "from skimage.data import astronaut\n",
+    "\n",
+    "# create the viewer on the Desktop and display the image\n",
+    "viewer = napari.view_image(astronaut(), rgb=True)"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.7.3"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}