Merge pull request #12 from jburel/cleaning

cleaning

docs/headless_notebook.rst

@@ -1,8 +1,8 @@
 Segment OMERO data using Fiji run headlessly in notebook
 ========================================================
 
-**Description:**
-----------------
+Description
+-----------
 
 The following examples follow up on the script shown in :doc:`threshold_scripting`.
 But, unlike in :doc:`threshold_scripting`, here, Fiji is included into a `Docker <https://www.docker.com/>`_ image and run in headless mode.
@@ -13,23 +13,19 @@ The scripts are embedded into a Jupyter Notebook. The Groovy language is used, w
 -  How to crop an image in OMERO using Fiji cropping functionality.
 
 
-**Setup:**
-----------
-Fiji has been installed in a Docker image.
+Setup
+-----
+Fiji has been installed in a Docker image using repo2docker.
 
-See also 
 
-- https://github.com/ome/training-notebooks/blob/master/Dockerfile
-- https://github.com/ome/training-notebooks/tree/master/Fiji
+Resources
+---------
 
-
-**Resources:**
-
--  Data: Samples images from the Image Data Resource (IDR) \ https://idr.openmicroscopy.org/webclient/?show=project-51
+-  Data: Samples images from the Image Data Resource (IDR) `idr0021 <https://idr.openmicroscopy.org/webclient/?show=project-51>`_.
 -  Macro: :download:`fiji-macro-segment.ijm <../scripts/fiji-macro-segment.ijm>`
 
-**Step-by-Step**
-----------------
+Step-by-Step
+------------
 
 #.  Create a Fiji macro, for example by recording it and save it locally. You can for example use adjusted macro created in :doc:`threshold_manual`. See :download:`fiji-macro-segment.ijm <../scripts/fiji-macro-segment.ijm>`.
 
@@ -43,9 +39,7 @@ See also
 
 #.  Open the *Attachments* harmonica in the right-hand panel and click on the plus icon. Browse and attach the :download:`fiji-macro-segment.ijm <../scripts/fiji-macro-segment.ijm>` to this Dataset as File Annotation.
 
-#.  Go to https://idr-analysis.openmicroscopy.org/training
-
-#.  Look under *Notebooks > Fiji* for *run_attached_macro.ipynb*.
+#.  Run the notebook `run_attached_macro.ipynb <https://mybinder.org/v2/gh/ome/omero-guide-fiji/master?filepath=notebooks/run_attached_macro.ipynb>`_.
 
 #.  Select the first Step and click on the Run button to execute each step in turn.
 
@@ -57,7 +51,7 @@ See also
 
 #.  The next cell is asking for input about the types of data which should be saved back to OMERO (ROIs, Results or Images). This is of course dependent on the type of results your Macro is producing in Fiji. For this example, we select ROIs and Results.
 
-#.  The script in the next cell will process all the Images in the specified         Dataset, applying threshold, analyzing particles, i.e. steps which are captured inside your macro file. Further, it will save ROIs back in OMERO and create a CSV to be attached to each image in that Dataset in OMERO.
+#.  The script in the next cell will process all the Images in the specified Dataset, applying threshold, analyzing particles, i.e. steps which are captured inside your macro file. Further, it will save ROIs back in OMERO and create a CSV to be attached to each image in that Dataset in OMERO.
 
 #.  Return to OMERO.web and open an Image from this Dataset in OMERO.iviewer.
 
@@ -77,9 +71,7 @@ See also
 #.  In the *Settings* tab, turning channels on/off will also show/hide ROIs
     assigned to those channels.
 
-#.  Go to https://idr-analysis.openmicroscopy.org/training
-
-#.  Look under *Notebooks > Fiji* for *crop_image.ipynb*.
+#.  Run the notebook `crop_image.ipynb <https://mybinder.org/v2/gh/ome/omero-guide-fiji/master?filepath=notebooks/crop_image.ipynb>`_.
 
 #.  Run through the notebook, logging in as previously and indicating the Image ID of the image you want to crop.
 
@@ -88,4 +80,3 @@ See also
 .. |image1| image:: images/threshold_script2.png
    :width: 1.89583in
    :height: 0.36458in
-

docs/index.rst

@@ -14,3 +14,8 @@ Contents:
    threshold_scripting
    headless_notebook
    imagej_python
+
+Contribute
+----------
+
+Changes to the documentation or the materials should be made directly in the `omero-guide-fiji repository <https://github.com/ome/omero-guide-fiji>`_.

docs/installation.rst

@@ -1,17 +1,17 @@
 How to install the OMERO plugin for Fiji/ImageJ
 ===============================================
 
-Description:
-------------
+Description
+-----------
 
-Fiji is a free open-source image processing package based on
-ImageJ, \ https://imagej.net/Fiji\ . The following workflow should how to
+`Fiji <https://imagej.net/Fiji>`__ is a free open-source image processing package based on
+ImageJ. The following workflow should how to
 install the OMERO plugin for Fiji and ImageJ.
 
 The OMERO plugin does not have yet and update site.
 
-**Setup step-by-step:**
------------------------
+Setup step-by-step
+------------------
 
 We assume that you have already Fiji/ImageJ installed locally.
 

docs/manual_analysis.rst

@@ -1,8 +1,8 @@
 Analyze manually OMERO data using the OMERO plugin for Fiji/ImageJ
 ==================================================================
 
-**Description:**
-----------------
+Description
+-----------
 
 The following workflows should work
 both with ImageJ and Fiji, after these have been correctly set up with
@@ -19,20 +19,20 @@ Using the User Interface of the OMERO plugin, we will show:
 
 -  How to import a newly created image from Fiji/ImageJ into OMERO.
 
-**Setup:**
-----------
+Setup
+-----
 
 -  Install Fiji on the local machine with the OMERO.insight-ij plugin.
    The installation instructions can be found at :doc:`installation`.
 
-**Resources:**
+Resources
+---------
 
--  Samples images from the Image Data Resource (IDR) \ https://idr.openmicroscopy.org/webclient/?show=project-51\ .
+-  Samples images from the Image Data Resource (IDR) `idr0021 <https://idr.openmicroscopy.org/webclient/?show=project-51>`__.
 
-..
 
-**Step-by-step:**
------------------
+Step-by-step
+------------
 
 **Example 1: ROIs and measurement creation**
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

docs/threshold_manual.rst

@@ -1,8 +1,8 @@
 Segment manually OMERO data using Fiji/ImageJ
 =============================================
 
-**Description:**
-----------------
+Description
+-----------
 
 The following workflows should work both with ImageJ and Fiji,
 after these have been correctly set up with
@@ -19,19 +19,20 @@ Using the User Interface of the OMERO plugin, we will show:
 
 -  How to record this workflow in Fiji/ImageJ, using the *Recorder* plugin, for later use.
 
-**Setup:**
-----------
+Setup
+-----
 
 -  Fiji has been installed on the local machine with the
    OMERO.insight-ij plugin. The installation instructions can be
    found at :doc:`installation`.
 
-**Resources:**
+Resources
+---------
 
--  Samples images from the Image Data Resource (IDR) \ https://idr.openmicroscopy.org/webclient/?show=project-51
+-  Samples images from the Image Data Resource (IDR) `idr0021 <https://idr.openmicroscopy.org/webclient/?show=project-51>`__.
 
-**Step-by-step:**
------------------
+Step-by-step
+------------
 
 #. Launch Fiji/ImageJ.
 

docs/threshold_scripting.rst

@@ -1,8 +1,8 @@
 Segment OMERO data using the Scripting editor in Fiji
 =====================================================
 
-**Description:**
-----------------
+Description
+-----------
 
 The following workflows should work in
 Fiji, after these have been correctly set up with the OMERO plugin for
@@ -27,31 +27,32 @@ Using the Scripting editor of Fiji, we will show:
 
    -  Save them as a CSV file and link it to the Dataset.
 
-**Setup:**
-----------
+Setup
+-----
 
 -  Install Fiji on the local machine with the OMERO.insight-ij plugin.
    The installation instructions can be found at :doc:`installation`.
 
-**Resources:**
+Resources
+---------
 
--  Data: Samples images from the Image Data Resource (IDR) \ https://idr.openmicroscopy.org/webclient/?show=project-51
+-  Data: Samples images from the Image Data Resource (IDR) `idr0021 <https://idr.openmicroscopy.org/webclient/?show=project-51>`_.
 
--  Java API documentation: \ https://docs.openmicroscopy.org/latest/omero/developers/Java.html
+-  `Java API documentation <https://docs.openmicroscopy.org/latest/omero/developers/Java.html>`__.
 
 -  Script: Groovy script for automatic segmentation of images from OMERO using Fiji
    -  :download:`analyse_dataset_save_rois_and_summary_table.groovy <../scripts/groovy/analyse_dataset_save_rois_and_summary_table.groovy>`.
 
-**Step-by-Step**
-----------------
+Step-by-Step
+------------
 
 We will now repeat the manual analysis :doc:`threshold_manual` on a
 Dataset using the scripting facility available in Fiji.
 
 Let’s go over the script to understand the logic and see how it matches
 the UI steps.
 
-This script explores the `JAVA API <https://docs.openmicroscopy.org/latest/omero/developers/Java.html>`_ using Groovy.
+This script explores the `JAVA API <https://docs.openmicroscopy.org/latest/omero/developers/Java.html>`__ using Groovy.
 
 It will process all the Images in the specified Dataset,
 applying threshold, analyzing particles and saving ROIs back in