From 45e67edfc94eb4ff4ece7ba535420c1bc5fb38c1 Mon Sep 17 00:00:00 2001 From: pwalczysko Date: Thu, 9 Apr 2026 11:38:40 +0100 Subject: [PATCH 1/2] livingobjects --- docs/view_mobie_zarr.rst | 4 ++-- notebooks/imagej_python_zarr.ipynb | 2 +- scripts/groovy/mobie_ome_zarr.groovy | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/view_mobie_zarr.rst b/docs/view_mobie_zarr.rst index 82ec93d..2a4e258 100644 --- a/docs/view_mobie_zarr.rst +++ b/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. diff --git a/notebooks/imagej_python_zarr.ipynb b/notebooks/imagej_python_zarr.ipynb index 9b3e90c..63827ca 100644 --- a/notebooks/imagej_python_zarr.ipynb +++ b/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", diff --git a/scripts/groovy/mobie_ome_zarr.groovy b/scripts/groovy/mobie_ome_zarr.groovy index 7f7b399..f97270f 100644 --- a/scripts/groovy/mobie_ome_zarr.groovy +++ b/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() From 5cd76b1e65bf2e0b0a0c11b6eeffc6c036c23a04 Mon Sep 17 00:00:00 2001 From: pwalczysko Date: Tue, 7 Apr 2026 11:08:33 +0100 Subject: [PATCH 2/2] Remove repo2docker and binder --- .github/workflows/repo2docker.yml | 23 ----------------------- README.md | 19 +------------------ docs/headless_notebook.rst | 2 +- 3 files changed, 2 insertions(+), 42 deletions(-) delete mode 100644 .github/workflows/repo2docker.yml diff --git a/.github/workflows/repo2docker.yml b/.github/workflows/repo2docker.yml deleted file mode 100644 index fe072f5..0000000 --- a/.github/workflows/repo2docker.yml +++ /dev/null @@ -1,23 +0,0 @@ -# Builds the repository using repo2docker - ---- -name: repo2docker - -on: - push: - pull_request: - schedule: - - cron: '0 0 * * 0' - -jobs: - build: - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v3 - - uses: actions/setup-python@v4 - - name: repo2docker install - run: | - pip install six chardet - pip install --upgrade jupyter-repo2docker - - name: Build container - run: repo2docker --no-run . diff --git a/README.md b/README.md index e0306e9..d92876a 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,5 @@ # 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). @@ -9,22 +7,7 @@ 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 diff --git a/docs/headless_notebook.rst b/docs/headless_notebook.rst index c127a47..880c54c 100644 --- a/docs/headless_notebook.rst +++ b/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