livingobjects

README.md

@@ -1,30 +1,13 @@
 # User guide for Fiji and OMERO
-[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/ome/omero-guide-fiji/master?filepath=notebooks)
 [![Documentation Status](https://readthedocs.org/projects/omero-guide-fiji/badge/?version=latest)](https://omero-guides.readthedocs.io/en/latest/fiji/docs/index.html)
-[![Actions Status](https://github.com/ome/omero-guide-fiji/workflows/repo2docker/badge.svg)](https://github.com/ome/omero-guide-fiji/actions)
 
 The documentation is deployed at [How to use Fiji](https://omero-guides.readthedocs.io/en/latest/fiji/docs/index.html).
 
 This guide demonstrates how to analyze data stored in OMERO in Fiji.
 This can be done using the User Interface or via the scripting facility in Fiji.
 
 
-To run the notebooks, you can either [run on mybinder.org](https://mybinder.org/v2/gh/ome/omero-guide-fiji/master?filepath=notebooks) or build locally with [repo2docker](https://repo2docker.readthedocs.io/).
-
-To build locally:
-
- * Install [Docker](https://www.docker.com/) if required
- * Create a virtual environment and install repo2docker from PyPI.
- * Clone this repository
- * Run  ``repo2docker``. 
- * Depending on the permissions, you might have to run the command as an admin
-
-```
-pip install jupyter-repo2docker
-git clone https://github.com/ome/omero-guide-fiji.git
-cd omero-guide-fiji
-repo2docker .
-```
+To run the notebooks, you can either [run on Google Colab](https://colab.research.google.com/) or build locally with [conda](https://docs.conda.io/en/latest/).
 
 This a Sphinx based documentation. 
 If you are unfamiliar with Sphinx, we recommend that you first read 

docs/headless_notebook.rst

@@ -15,7 +15,7 @@ The scripts are embedded into a Jupyter Notebook. The Groovy language is used, w
 
 Setup
 -----
-Fiji has been installed in a Docker image using repo2docker.
+Fiji has been installed in a Docker image.
 
 
 Resources

docs/view_mobie_zarr.rst

@@ -52,7 +52,7 @@ Step-by-step
 
 #. In the text field, you can click `Browse` to open local data or enter the desired URL e.g.
 
- ``https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0062A/6001240.zarr``
+ ``https://livingobjects.ebi.ac.uk/idr/zarr/v0.4/idr0062A/6001240.zarr``
 
 #. If you Click the `OK`` button tbis will open the image in `BigDataViewer`. You can also click the `Detect datasets` button to inspect the
    content of the zarr file, such as individual pyramid arrays and labels. You can select multiple items, for example to open
@@ -74,6 +74,6 @@ Step-by-step
 
 #. In the text field, enter the desired URL e.g.
 
- ``https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0062A/6001240.zarr``
+ ``https://livingobjects.ebi.ac.uk/idr/zarr/v0.4/idr0062A/6001240.zarr``
 
 #. Click the `OK` button.

notebooks/imagej_python_zarr.ipynb

@@ -129,7 +129,7 @@
    ],
    "source": [
     "def load_binary_from_s3(id, resolution='0'):\n",
-    "    endpoint_url = 'https://uk1s3.embassy.ebi.ac.uk/'\n",
+    "    endpoint_url = 'https://livingobjects.ebi.ac.uk/'\n",
     "    root = 'idr/zarr/v0.1/%s.zarr/%s/' % (id, resolution)\n",
     "    data = da.from_zarr(endpoint_url + root)\n",
     "    with ProgressBar():\n",

scripts/groovy/mobie_ome_zarr.groovy

@@ -32,6 +32,6 @@
 import org.embl.mobie.OMEZarrViewer
 import org.embl.mobie.io.ome.zarr.openers.OMEZarrS3Opener
 
-filePath = "https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0083A/9822152.zarr"      
+filePath = "https://livingobjects.ebi.ac.uk/idr/zarr/v0.4/idr0083A/9822152.zarr"
 viewer = new OMEZarrViewer(OMEZarrS3Opener.readURL(filePath))
 viewer.show()