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Data management additions #4

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fix layout issue
jburel committed Jun 26, 2020
commit 43d7cc445fba0c4f9f71bf46a6fe28aeb6742491
42 changes: 20 additions & 22 deletions docs/data-management.rst
Original file line number Diff line number Diff line change
@@ -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.
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**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: