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Add note about zarr etc requirement for export script with zarr images #686

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c25a3b3
Add note about zarr etc requirement for export script with zarr images
will-moore Apr 23, 2026
94ae5c8
Move script dependencies install before script install
will-moore Apr 23, 2026
fd09cda
Add 'v8.0.1 release candidate only' to OME-Zarr support in README
will-moore Apr 23, 2026
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40 changes: 21 additions & 19 deletions README.rst
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Expand Up @@ -82,6 +82,25 @@ This section assumes that an OMERO.server is already installed.
Figures can be exported as PDF or TIFF files using a script that runs on the OMERO.server. This script needs to be uploaded to the OMERO.server and its dependencies
installed in the OMERO.server virtual environment.

First install the script's dependencies:

* Install `reportlab <https://bitbucket.org/rptlab/reportlab>`_ PDF python package.
This needs to be installed in the virtual environment where the ``OMERO.server`` is installed. Depending on your install, you may need to
call ``pip`` with, for example: ``/path/to_server_venv/venv/bin/pip install ...``. The install of `Python Markdown <https://python-markdown.github.io/>`_ is optional
but is required to format any figure legends that use Markdown syntax.

::

$ pip install reportlab markdown

* Optional (v8.0.1 release candidate only): If your figure contains OME-Zarr images, you will also need to install the dependencies for rendering
OME-Zarr images in the export script. These are `zarr`, `dask` and `fsspec[http]`:

::

$ pip install zarr dask fsspec[http]


The script can be uploaded using various workflows, all of which require you to have the correct admin privileges.

*Option 1*: Log in to the webclient as an Admin and open the OMERO.figure app. If the OMERO script is not found or is not up to date, you will
Expand All @@ -105,26 +124,9 @@ Connect to the OMERO server and upload the script via the CLI. It is important t
*Option 3*: Alternatively, before starting the OMERO.server, copy the script from the figure install
``/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py`` to the OMERO.server ``path/to/OMERO.server/lib/scripts/omero/figure_scripts``. Then restart the OMERO.server.

Now install the script's dependencies:


* Install `reportlab <https://bitbucket.org/rptlab/reportlab>`_ PDF python package.
This needs to be installed in the virtual environment where the ``OMERO.server`` is installed. Depending on your install, you may need to
call ``pip`` with, for example: ``/path/to_server_venv/venv/bin/pip install ...``

::

$ pip install reportlab

* Optional: Figure legends can be formatted using Markdown syntax. To see this correctly in the exported PDF info page, we need `Python Markdown <https://python-markdown.github.io/>`_:

::

$ pip install markdown


Run Figure export locally
-------------------------
Run Figure export locally (v8.0.1 release candidate only)
---------------------------------------------------------

If your figure contains only OME-Zarr images (no images from OMERO), then
the export script can be run locally to convert a figure JSON file to PDF or TIFF.
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