Cleaning

docs/annotate.rst

@@ -4,12 +4,12 @@ Annotate Data and Filter using Annotations
 In this section, we show various types of annotations supported in
 OMERO and how to use them.
 
-**Description**
----------------
+Description
+-----------
 
 We will show:
 
--  How to annotate Images, Datasets and Projects with
+-  How to annotate Images, Datasets and Projects with:
 
    -  Tags
 
@@ -19,25 +19,25 @@ We will show:
 
    -  Ratings
 
--  How to filter thumbnails in the central pane of OMERO.web for
+-  How to filter thumbnails in the central pane of OMERO.web for:
 
    -  Tags
 
    -  Key-Value Pairs
 
    -  Ratings
 
-**Setup**
----------
+Setup
+-----
 
--  The data used are from the siRNAi-HeLa folder available at \ https://downloads.openmicroscopy.org/images/DV/siRNAi-HeLa/
+-  The data used are from the `siRNAi-HeLa <https://downloads.openmicroscopy.org/images/DV/siRNAi-HeLa>`_ folder.
 
--  The tags and ratings were added manually, then propagated for all users on the OMERO.server using the script \ https://github.com/ome/training-scripts/blob/master/maintenance/scripts/copy_tags_ratings.py
+-  The tags and ratings were added manually, then propagated for all users on the OMERO.server using the script `copy_tags_ratings.py <https://github.com/ome/training-scripts/blob/master/maintenance/scripts/copy_tags_ratings.py>`_.
 
--  The Key-Value Pairs were added to the images in the siRNAi-HeLa Dataset for all users using the script \ https://github.com/ome/training-scripts/blob/master/maintenance/scripts/key_value_pairs.py
+-  The Key-Value Pairs were added to the images in the siRNAi-HeLa Dataset for all users using the script `key_value_pairs.py <https://github.com/ome/training-scripts/blob/master/maintenance/scripts/key_value_pairs.py>`_.
 
-**Step-by-step**
-----------------
+Step-by-step
+------------
 
 #. Open a browser and enter the provided URL
 
@@ -47,15 +47,15 @@ We will show:
 
    - Select one or more Images in the siRNAi-HeLa Dataset of cells which appear to be in metaphase.
 
-   - Choose the Tag option in the right-hand General tab and click [ + ] to launch the Tag dialog.
+   - Choose the Tag option in the right-hand ``General`` tab and click ``[ + ]`` to launch the Tag dialog.
 
    - Choose the existing Metaphase from the list of Tags (to filter, type above the list).
 
-   - Click > to move it to the right column, then click OK.
+   - Click > to move it to the right column, then click ``OK``.
 
 #. Let’s now add Key-Value Pairs
 
-   - Select an Image from the Dataset and in the right-hand pane in General tab, click the harmonica Key-Value Pairs.
+   - Select an Image from the Dataset and in the right-hand pane in ``General`` tab, click the harmonica Key-Value Pairs.
 
       |image0|
 
@@ -69,7 +69,7 @@ We will show:
 
    - Images can also be filtered by Name, Tag, Key-Value pairs or Rating in the centre pane, using the Add filter chooser above the thumbnails.
 
-   - For example, choose Tag and then select Metaphase from the list of Tags to show the images we tagged earlier.
+   - For example, choose ``Tag`` and then select ``Metaphase`` from the list of Tags to show the images we tagged earlier.
 
    - Or choose to filter by Key-Values. You can then filter by a particular Key. If you select a Key where all the
      values are numbers, you can filter for those that are greater than, less than or equal to a threshold value.

docs/conf.py

@@ -50,7 +50,7 @@
 
 # General information about the project.
 project = u'OMERO general introduction guide'
-copyright = u'2019, Open Microscopy Environment'
+copyright = u'2019-2020, Open Microscopy Environment'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the

docs/data-management.rst

@@ -6,42 +6,40 @@ such as browsing, navigating to others’ data, and changing the display
 of the images in OMERO. The example here uses OMERO.web, but majority of
 the features described here are also present in OMERO.insight.
 
-**Description**
----------------
+Description
+-----------
 
 We will show:
 
--  How to browse data in OMERO.web, navigating to yours and other users’ images
+-  How to browse data in OMERO.web, navigating to yours and other users’ images.
 
--  How to use the basic layout of OMERO.web
+-  How to use the basic layout of OMERO.web.
 
--  How to use the Preview panel
+-  How to use the Preview panel.
 
--  How to adjust the rendering settings of yours and other users’ images from the Preview panel
+-  How to adjust the rendering settings of yours and other users’ images from the Preview panel.
 
-**Setup**
----------
-
-OMERO.server has been installed and provisioned using the Ansible software, the corresponding playbook
+Setup
+-----
 
--  https://github.com/ome/prod-playbooks/blob/master/omero/training-server/playbook.yml
+OMERO.server has been installed and provisioned using an `Ansible playbook <https://github.com/ome/prod-playbooks/blob/master/omero/training-server/playbook.yml>`_.
 
-**Resources**
--------------
+Resources
+---------
 
--  All data have been pre-imported. For more details, go to: https://github.com/ome/training-repos/blob/master/data.md
+-  All data have been pre-imported. For more details, look at `data.md <https://github.com/ome/training-repos/blob/master/data.md>`_.
 
--  To import images and metadata, scripts were used. For more details, go to: https://github.com/ome/training-scripts/tree/master/maintenance
+-  To import images and metadata, scripts were used. For more details, check the `maintenance scripts <https://github.com/ome/training-scripts/tree/master/maintenance>`_.
 
--  For import of images, the main script used was: https://github.com/ome/training-scripts/blob/master/maintenance/scripts/in_place_import_as.sh
+-  For import of images, we use `in_place_import_as.sh <https://github.com/ome/training-scripts/blob/master/maintenance/scripts/in_place_import_as.sh>`_.
 
--  The cooperation in OMERO is described in https://docs.openmicroscopy.org/latest/omero/sysadmins/server-permissions.html
+-  The cooperation in OMERO is described in `Groups and permissions system <https://docs.openmicroscopy.org/latest/omero/sysadmins/server-permissions.html>`_.
 
-**Step-by-Step**
-----------------
+Step-by-Step
+------------
 
-**Data layout and ownership, usernames**
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+Data layout and ownership, usernames
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 All images for this workshop have been pre-imported for you into the
 OMERO.server. For training purposes, we prepared 50 users on the
@@ -81,7 +79,7 @@ Browsing and rendering
 
 #.  These represent imported Images. The original Images are stored on the server and the generated thumbnails allow us to browse them.
 
-#.  Bio-Formats,\ https://www.openmicroscopy.org/bio-formats/\ , is used to read the pixel-data and metadata from over 150 different image formats, including multi-z timelapse images with many channels, they are referenced as 5D Images. Large pathology and medical images are also supported.
+#.  `Bio-Formats <https://www.openmicroscopy.org/bio-formats/>`_ is used to read the pixel-data and metadata from over 150 different image formats, including multi-z timelapse images with many channels, they are referenced as 5D Images. Large pathology and medical images are also supported.
 
 #.  Select an Image. In the right-hand pane, metadata read by Bio-Formats and stored in a relational database is displayed:
 

docs/search-omero.rst

@@ -3,32 +3,32 @@ Search for Data
 
 In this section, we present the server-wide search in OMERO. This is an additional option for data management, which complements filtering, mining and using annotations to organize your data, which are described elsewhere in :doc:`annotate`.
 
-**Description**
----------------
+Description
+-----------
 
 We will show:
 
--  How to start a search in OMERO.web
+-  How to start a search in OMERO.web.
 
--  How to search for objects annotated with a specific Key-Value Pair
+-  How to search for objects annotated with a specific Key-Value Pair.
 
--  How to use Advanced Search
+-  How to use Advanced Search.
 
-   -  How to search for terms in specific fields e.g. "name"
+   -  How to search for terms in specific fields e.g. "name".
 
-   -  How to combine search terms using AND
+   -  How to combine search terms using AND.
 
-   -  How to combine search terms using AND NOT
+   -  How to combine search terms using AND NOT.
 
-**Setup**
----------
+Setup
+-----
 
--  The data used are from the siRNAi-HeLa folder available at \ https://downloads.openmicroscopy.org/images/DV/siRNAi-HeLa/
+-  The data used are from the `siRNAi-HeLa <https://downloads.openmicroscopy.org/images/DV/siRNAi-HeLa>`_ folder.
 
--  The Key-Value Pairs were added to the images in the siRNAi-HeLa Dataset for all users using the script \ https://github.com/ome/training-scripts/blob/master/maintenance/scripts/key_value_pairs.py
+-  The Key-Value Pairs were added to the images in the siRNAi-HeLa Dataset for all users using the script `key_value_pairs.py <https://github.com/ome/training-scripts/blob/master/maintenance/scripts/key_value_pairs.py>`_.
 
-**Step-by-Step**
-----------------
+Step-by-Step
+------------
 
 #.  Open a browser and enter the provided URL
 
@@ -46,13 +46,13 @@ We will show:
 
 #.  Now you should find only 21 images.
 
-#.  Click on the “Advanced search” tab in the search results.
+#.  Click on the "Advanced search" tab in the search results.
 
 #. Enter mitomycin-A:0mM AND name:VRAQ which will narrow down your previous search for mitomycin-A:0mM to objects which also have VRAQ in their name.
 
 #. You should see 5 results now.
 
-#. Enter mitomycin-A:0mM AND NOT name:VRAQ which will reject all objects which have VRAQ in their name and find only the ones which are named differently.
+#. Enter ``mitomycin-A:0mM AND NOT name:VRAQ`` which will reject all objects which have VRAQ in their name and find only the ones which are named differently.
 
 #. You should see 16 results now.