Merge pull request #7 from jburel/python

Python

docs/imagej_python.rst

@@ -0,0 +1,42 @@
+Use ImageJ in Python
+====================
+
+Description:
+------------
+
+This section shows how to use ImageJ as a Python library to analyze data in OMERO.
+
+Using the Python API allows us to easily load the 2D-plane we need to see or analyze.
+This is much easier that when using the Java API and Bio-Formats plugin.
+
+We will show in the notebooks:
+
+- How to start ImageJ in Python
+
+- How to load data from OMERO
+
+- How to run ImageJ macro from Python
+
+Setup
+-----
+
+In this case, Fiji has been installed locally. It is possible to install Fiji "on the fly",
+see `ImageJ Tutorials <https://nbviewer.jupyter.org/github/imagej/tutorials/blob/master/notebooks/ImageJ-Tutorials-and-Demo.ipynb>`_ for more options.
+
+Install omero-py and `pyimagej <https://pypi.org/project/pyimagej/>`_ via Conda:
+
+- Install `Miniconda <https://docs.conda.io/en/latest/miniconda.html>`_ if necessary.
+
+- Create a programming environment using Conda and activate it::
+
+    $ conda create -n fiji_python python=3.6
+
+    $ conda activate fiji_python
+
+- Install omero-py and `pyimagej <https://pypi.org/project/pyimagej/>`_::
+
+    $ conda install -c conda-forge pyimagej
+
+    $ conda install -c ome omero-py
+
+

docs/index.rst

@@ -13,3 +13,4 @@ Contents:
    threshold_manual
    threshold_scripting
    headless_notebook
+   imagej_python