Merge pull request #32 from mahyar-osn/master

Updates on the use cases

source/MouseHeart.rst

@@ -1,6 +1,12 @@
 Mapping the Mouse Heart Neurites from Image to Scaffold
 ========================================================
 
+.. |scaffold-icon| image:: /_images/scaffold_icon.png
+                      :width: 2 em
+
+.. |open-control| image:: /_images/open_control.png
+                      :width: 2 em
+
 .. contents:: Contents: 
    :local:
    :depth: 2
@@ -25,59 +31,66 @@ Below is an **introductory video** which explains the mapping of the mouse heart
 
 .. raw:: html
 
-	<iframe width="560" height="315" src="https://www.youtube.com/embed/B0JKztUZFio" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
+    <iframe width="560" height="315" src="https://www.youtube.com/embed/B0JKztUZFio" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
 
-.. todo::
-	This document guides a user of the SPARC Data Portal through the steps required to .......
-
-.. todo::
-    add link to final portal URL that takes user straight to this dataset display.
 
 Step-by-step instructions 
 *************************
-.. todo:: 
-		Write steps + screenshots
 
 Follow these step-by-step instructions to familiarise yourself with the flow of the web interface.
 
-Explain the steps to be followed by the end user on the web interface. 
-
-#. Step 1 ....
 
-Add screenshot
+**Step 1**. The default **Result** column displays some of the use cases available on the portal. Click on
+*Mapping the Mouse Heart Neurites from Image to Scaffold* box.
 
-.. .. figure:: _images/snip
+.. figure:: _images/use_case_3/Slide1.PNG
    :figwidth: 61%
    :width: 51%
    :align: center
 
-#. Step 2 ....
+**Step 2** Now click on the |scaffold-icon| to open the **Scaffold Viewer** tab to visualise the heart scaffold.
 
-Add screenshot 
+.. figure:: _images/use_case_3/Slide2.PNG
+   :figwidth: 61%
+   :width: 51%
+   :align: center
 
-Working with the interface
-**************************
-This section explains how to use more specific features of the interface.
+**Step 3**. In the **Scaffold Viewer** tab, there are three objects visible: 1) fitted heart scaffold, 2) sham heart 44
+neurite tracing, 3) sham heart 4 neurite tracing.
 
-.. todo::
-      Highlight features/capabilities that are particular to this use-case.
-
-:ref:`Flatmap-Viewer`
-^^^^^^^^^^^^^^^^^^^^^
-The :ref:`Flatmap-Viewer` represents a high-level view of overall connectivity of the autonomic nervous system.
-
-:ref:`Scaffold-Viewer`
-^^^^^^^^^^^^^^^^^^^^^^
-:ref:`Scaffold-Viewer` is used to view the anatomical organ scaffold of the specific organ selected on the Flatmap.
-
-:ref:`Data-Viewer`
-^^^^^^^^^^^^^^^^^^
-This viewer is used to view the *Electrocardiograph* data recorded with the experiment video. Refer the section :ref:`Data-Viewer`.
+.. figure:: _images/use_case_3/Slide3.PNG
+   :figwidth: 61%
+   :width: 51%
+   :align: center
 
+**Step 4**. Click on |open-control| to open the control panel.
 
+.. figure:: _images/use_case_3/Slide4.PNG
+   :figwidth: 61%
+   :width: 51%
+   :align: center
 
+**Step 5**. Turn off Sham 4 neurons to only visualise the scaffold and Sham 44 neurons.
 
+.. figure:: _images/use_case_3/Slide5.PNG
+   :figwidth: 61%
+   :width: 51%
+   :align: center
+
+**Step 6**. Turn Sham 4 neurons back on and now turn off Sham 44 neurons to visualise the registered neurons on the scaffold
+surface.
+
+.. figure:: _images/use_case_3/Slide6.PNG
+   :figwidth: 61%
+   :width: 51%
+   :align: center
+
+**Step 7**. To visualise only the neurons, turn off the scaffold.
 
+.. figure:: _images/use_case_3/Slide7.PNG
+   :figwidth: 61%
+   :width: 51%
+   :align: center
 
 
 

source/PigHeart.rst

@@ -1,6 +1,12 @@
 Mapping Cardiac Electromechanics in the Pig
 ===========================================
-
+.. |open-control| image:: /_images/open_control.png
+                      :width: 2 em
+
+.. |scaffold-map-icon| image:: /_images/scaffold_map_icon.png
+						:width: 2 em
+
+
 .. contents:: Contents: 
    :local:
    :depth: 2
@@ -9,9 +15,18 @@ Mapping Cardiac Electromechanics in the Pig
 Overview
 ********
 
-Pig heart electromechanical data from the Shivkumar/Ardell group is displayed on a 3D pig heart scaffold. The deforming geometry of the pig heart is fitted through the cardiac cycle with the pig heart scaffold. Electrophysiological measurements from two 64-electrode patches, one on the left ventricle (LV) and one on the right ventricle (RV), are fitted as time-varying fields via scaffold parameters and shown on the LV and RV epicardial surfaces, respectively, of the beating heart model. *Note* that these electromechanical data, fitted to the 3D scaffold, are from the same pig heart and include both physiological normal contracting heart beats and the whole heart response to stellate stimulation. This use-case demonstrates the use of the scaffold to merge two types of data set (one mechanical and one electrophysiological) and begins to illustrate the connection between stimulation of the peripheral nervous system and the response at the whole heart level.
+Pig heart electromechanical data from the Shivkumar/Ardell group is displayed on a 3D pig heart scaffold.
+The deforming geometry of the pig heart is fitted through the cardiac cycle with the pig heart scaffold.
+Electrophysiological measurements from two 64-electrode patches, one on the left ventricle (LV) and one on the right
+ventricle (RV), are fitted as time-varying fields via scaffold parameters and shown on the LV and RV epicardial surfaces,
+respectively, of the beating heart model. *Note* that these electromechanical data, fitted to the 3D scaffold, are from
+the same pig heart and include both physiological normal contracting heart beats and the whole heart response to stellate
+stimulation. This use-case demonstrates the use of the scaffold to merge two types of data set (one mechanical and one
+electrophysiological) and begins to illustrate the connection between stimulation of the peripheral nervous system and
+the response at the whole heart level.
 
-This document guides a user of the SPARC Data Portal through the steps required to discover some data looking at autonomic control of the heart.
+This document guides a user of the SPARC Data Portal through the steps required to discover some data looking at
+autonomic control of the heart.
 
 .. todo::
     add link to final portal URL that takes user straight to this dataset display.
@@ -21,50 +36,48 @@ Step-by-step instructions
 
 Follow these step-by-step instructions to familiarise yourself with the flow of the web interface.
 
-.. todo:: check these steps and update screen shots
-
-**Step 1:** Allow a few seconds of time for models to load.
+**Step 1:** The default **Result** column displays some of the use cases available on the portal. Click on
+*Mapping Cardiac Electromechanics in the Pig* box.
 
 
-.. figure:: _images/ph_loading.png
+.. figure:: _images/pig_slide1.png
    :figwidth: 95%
    :width: 90%
    :align: center
 
-**Step 2:** Select a *node* to open it's ECG data in a seperate viewer i.e. the Electrode Data Viewer.
+**Step 2:** Now click on the |scaffold-icon| to open the **Scaffold Viewer** tab to visualise the heart scaffold.
 
-.. figure:: _images/ph_node.png
+.. figure:: _images/pig_slide2.png
    :figwidth: 95%
    :width: 90%
    :align: center
 
-.. figure:: _images/ph_ecg.png
+**Step 3:** In the **Scaffold Viewer** tab, a 3D pig heart scaffold has been fitted to the 2D video data.
+In addition a 64-electrode patch mesh has been constructed from the original electrode patch on the surface of the left
+ventricular epicardium. Electro-physiological data recorded from this patch has been registered on the mesh and a field
+is displayed on the surface of this mesh. This mesh is then *embedded* on the corresponding surface of the scaffold.
+
+Press *play* to see the video.
+
+.. figure:: _images/pig_slide3.png
    :figwidth: 95%
    :width: 90%
    :align: center
-
-**Step 3:** Navigate through the video with the play button and slider.
 
-.. figure:: _images/ph_slider_1.png
+**Step 4:** In the current version, the scaffold has only been fitted to the video data through anisotropic scaling and
+some shear. This was a limitation as only one view angle was available. In future, a stereo camera system will be installed
+to reconstruct a 3D view of the beating heart in order to accurately fit the scaffold and capture the deformation of cardiac
+tissue.
+
+.. figure:: _images/pig_slide4.gif
    :figwidth: 95%
    :width: 90%
    :align: center
 
-Working with the interface
-**************************
-This section explains how to use more specific features of the interface.
+**Step 4:** By clicking on |open-control| you can control visibility of each of the graphical objects in the scene.
+
+.. figure:: _images/pig_slide5.png
+   :figwidth: 95%
+   :width: 90%
+   :align: center
 
-.. todo::
-      Highlight features/capabilities that are particular to this use-case.
-
-:ref:`Flatmap-Viewer`
-^^^^^^^^^^^^^^^^^^^^^
-The :ref:`Flatmap-Viewer` represents a high-level view of overall connectivity of the autonomic nervous system.
-
-:ref:`Scaffold-Viewer`
-^^^^^^^^^^^^^^^^^^^^^^
-:ref:`Scaffold-Viewer` is used to view the anatomical organ scaffold of the specific organ selected on the Flatmap.
-
-:ref:`Data-Viewer`
-^^^^^^^^^^^^^^^^^^
-This viewer is used to view the *Electrocardiograph* data recorded with the experiment video. Refer the section :ref:`Data-Viewer`.