Merge pull request #16 from jburel/doc_update

Doc update
ome · May 18, 2020 · 2043b02 · 2043b02
2 parents 77da0e1 + 86d5660
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diff --git a/docs/gettingstarted.rst b/docs/gettingstarted.rst
@@ -18,7 +18,7 @@ We will show:
 
 - How to run ilastik using its Python API.
 
-- How to save the generated results as OMERO images.
+- How to save the generated results as OMERO images. If you are accessing a public resource e.g. idr.openmicroscopy.org, this step will not work.
 
 **Setup**
 ---------
@@ -34,7 +34,7 @@ We will use an ilastik project created with ilastik version 1.3.3 to analyze 3D
 - IDR data \ https://idr.openmicroscopy.org/webclient/?show=project-801
 
 For convenience, the IDR data have been imported into the training
-OMERO.server. This is only because we cannot save results back to IDR
+OMERO.server. This is **only** because we **cannot** save results back to IDR
 which is a read-only OMERO.server.
 
 **Step-by-Step**

diff --git a/docs/ilastik_fiji.rst b/docs/ilastik_fiji.rst
@@ -4,7 +4,7 @@ Use ilastik as a Fiji plugin and OMERO
 **Description**
 ---------------
 
-In this section, we will show how to use ilastik user interface to
+In this section, we will show how to use the ilastik user interface to
 perform segmentations on multi-z images stored in OMERO. The connection
 between OMERO and ilastik is facilitated via Fiji, for which both OMERO
 and ilastik have plugins. The segmentation steps in this part are

diff --git a/docs/ilastik_parallel.rst b/docs/ilastik_parallel.rst
@@ -6,7 +6,7 @@ Run ilastik in parallel using dask
 ---------------
 
 We will show how to use `dask <https://dask.org/>`_ to analyze images in parallel
-using ilastik. Binary data are stored in a public S3 repository in the Zarr format.
+using the ilastik API. Binary data are stored in a public S3 repository in the Zarr format.
 
 
 **Setup**
@@ -35,14 +35,12 @@ Load the images:
     :start-after: # Load-images
     :end-before: # Load-binary
 
-
 Define the analysis function:
 
 .. literalinclude:: ../scripts/pixel_classification_zarr_parallel.py
     :start-after: # Analyze-data
     :end-before: # Prepare-call
 
-
 Helper function load the binary as a numpy array from the Zarr storage format:
 
 .. literalinclude:: ../scripts/pixel_classification_zarr_parallel.py
@@ -68,7 +66,6 @@ We wait until this work is done and gather the results to our local process:
     :start-after: # Gather
     :end-before: # Disconnect
 
-
 When done, close the session:
 
 .. literalinclude:: ../scripts/pixel_classification_zarr_parallel.py

diff --git a/docs/index.rst b/docs/index.rst
@@ -2,6 +2,7 @@ ilastik
 =======
 
 ilastik is a free open-source interactive learning and segmentation toolkit, with which can be used to leverage machine learning algorithms to easily segment, classify, track and count cells or other experimental data. For more details go to see \ https://www.ilastik.org/\.
+We will show how to analyze data stored in OMERO, using the ilastik user interface, Fiji and the OMERO ImageJ plugin. We will then also show how to analyze images using the ilastik API and OMERO.py API.
 
 Contents:
 

diff --git a/docs/setup.rst b/docs/setup.rst
@@ -2,7 +2,7 @@ Install ilastik and OMERO Python bindings
 ==========================================
 
 In this section, we show how to install ilastik in a `Conda <https://conda.io/en/latest/>`_ environment.
-We will use the ilastik API to analyze data stored in an OMERO server.
+We will use the ilastik API to analyze data stored in an OMERO server. We will use OMERO.py to interact with the OMERO server.
 
 **Setup**
 ---------
@@ -12,7 +12,9 @@ Conda manages programming environments in a manner similar to
 `virtualenv <https://virtualenv.pypa.io/en/stable/>`_.
 You can install the various dependencies following the steps below (Option 1) or build locally a Docker Image
 using ``repo2docker`` (Option 2). When the installation is done, you should be ready to use the ilastik API and OMERO, see :doc:`gettingstarted`.
-:
+
+The installation below is needed to run the scripts and/or notebooks. If you wish to start your own environment without the scripts/notebooks, copy locally into an ``environment.yml`` file the content of 
+`binder/environment.yml <https://raw.githubusercontent.com/ome/omero-guide-ilastik/master/binder/environment.yml>`_, remove or add the dependencies you need and run the commands below to create a conda environment.
 
 *Option 1*
 ~~~~~~~~~~