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ome · Jun 12, 2020 · 29d3b23 · 29d3b23
1 parent 2a766fb
commit 29d3b23
Showing 1 changed file with 8 additions and 8 deletions.
diff --git a/docs/metadata.rst b/docs/metadata.rst
@@ -23,27 +23,27 @@ Resources
 
 -  Documentation:
 
-   -  https://docs.openmicroscopy.org/omero/latest/users/cli/installation.html
+   -  `CLI installation <https://docs.openmicroscopy.org/omero/latest/users/cli/installation.html>`_
 
-   -  `https://docs.openmicroscopy.org/omero/latest/users/cli/index.html <https://docs.openmicroscopy.org/omero/latest/users/cli/index.html>`__
+   -  `CLI <https://docs.openmicroscopy.org/omero/latest/users/cli/index.html>`__
 
 -  Data: example images from
 
-   -  IDR data https://idr.openmicroscopy.org/webclient/?show=project-51
-   -  siRNAi-HeLa dataset from https://downloads.openmicroscopy.org/images/DV/siRNAi-HeLa/
+   -  IDR data `idr0021-lawo-pericentriolarmaterial/experimentA <https://idr.openmicroscopy.org/webclient/?show=project-51>`_
+   -  `siRNAi-HeLa <https://downloads.openmicroscopy.org/images/DV/siRNAi-HeLa/>`_ dataset
 
 -  Metadata plugin for OMERO
 
    - https://pypi.org/project/omero-metadata/
 
 -  Bulkmap config yml files defining the various Key-Value pairs parameters, such as the groups and other parameters.
 
-   - https://github.com/IDR/idr0021-lawo-pericentriolarmaterial/blob/9479af85f19487f215e3dfdd31a1b587370ed3cf/experimentA/idr0021-experimentA-bulkmap-config.yml
+   - `idr0021-experimentA-bulkmap-config.yml <https://github.com/IDR/idr0021-lawo-pericentriolarmaterial/blob/9479af85f19487f215e3dfdd31a1b587370ed3cf/experimentA/idr0021-experimentA-bulkmap-config.yml>`_
    - :download:`simple-annotation-bulkmap-config.yml <../scripts/simple-annotation-bulkmap-config.yml>`
 
 -  Annotation CSV files define the content of OMERO.tables for each image.
 
-   - https://github.com/IDR/idr0021-lawo-pericentriolarmaterial/blob/9479af85f19487f215e3dfdd31a1b587370ed3cf/experimentA/idr0021-experimentA-annotation.csv
+   - `idr0021-experimentA-annotation.csv <https://github.com/IDR/idr0021-lawo-pericentriolarmaterial/blob/9479af85f19487f215e3dfdd31a1b587370ed3cf/experimentA/idr0021-experimentA-annotation.csv>`_
    - :download:`simple-annotation.csv <../scripts/simple-annotation.csv>`
    - :download:`four-images.csv <../scripts/four-images.csv>`
 
@@ -52,7 +52,7 @@ Setup
 
 **Metadata plugin installation**
 
-- Go to the environment where you installed your OMERO.cli as specified under -  https://docs.openmicroscopy.org/omero/latest/users/cli/installation.html.
+- Go to the environment where you installed your OMERO.cli as specified under - `CLI installation <https://docs.openmicroscopy.org/omero/latest/users/cli/installation.html>`_.
 
 - Activate the virtual environment.
 
@@ -69,7 +69,7 @@ Step-by-step
 
     $ export PATH=/opt/omero/server/venv3/bin:$PATH
 
-#.  Download the CSV from `idr0021-experimentA-annotation.csv <https://github.com/IDR/idr0021-lawo-pericentriolarmaterial/blob/9479af85f19487f215e3dfdd31a1b587370ed3cf/experimentA/idr0021-experimentA-annotation.csv>`_ if you have access to the `idr0021 <https://idr.openmicroscopy.org/webclient/?show=project-51>`_ data  in your OMERO.server. Alternatively, download :download:`simple-annotation.csv <../scripts/simple-annotation.csv>`, which will allow you to work with the siRNAi-HeLa dataset, which you can download from https://downloads.openmicroscopy.org/images/DV/siRNAi-HeLa/.
+#.  Download the CSV from `idr0021-experimentA-annotation.csv <https://github.com/IDR/idr0021-lawo-pericentriolarmaterial/blob/9479af85f19487f215e3dfdd31a1b587370ed3cf/experimentA/idr0021-experimentA-annotation.csv>`_ if you have access to the `idr0021 <https://idr.openmicroscopy.org/webclient/?show=project-51>`_ data  in your OMERO.server. Alternatively, download :download:`simple-annotation.csv <../scripts/simple-annotation.csv>`, which will allow you to work with the `siRNAi-HeLa <https://downloads.openmicroscopy.org/images/DV/siRNAi-HeLa/>`_ dataset.
 
 #.  The variable ``$ID`` below is the ID of the Project, in this example case it is the Project containing the idr0021 study. If you are working with the siRNAi-HeLa data, replace in the following example the "Project" with a "Dataset" and the ``idr0021-experimentA-annotation.csv`` with ``simple-annotation.csv``. To add annotations from a local CSV file to the images in the said Project or Dataset in the form of OMERO.tables, run::