Merge pull request #30 from shsa992/master

updated screenshots for Stellate, Lungs,Colon
ABI-Software · Jul 26, 2019 · d15c738 · d15c738
2 parents db6b75b + d23f258
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diff --git a/source/MouseBrainStemLungs.rst b/source/MouseBrainStemLungs.rst
@@ -3,7 +3,9 @@ Mapping Gene Expression in the Mouse Lungs from Images to Scaffold
 ===================================================================		
 .. |open-control| image:: /_images/open_control.png
                       :width: 2 em	
-
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+.. |scaffold-map-icon| image:: /_images/scaffold_map_icon.png					  
+						:width: 2 em				  
 .. contents:: Contents: 
    :local:
    :depth: 2
@@ -26,10 +28,6 @@ Below is an **introductory video** which explains how an anatomically based 3D t
 	<iframe width="560" height="315" src="https://www.youtube.com/embed/8FDcPuwWAQo" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>   
 
 
-.. todo::
-	provide demo link 
-
-
 Step-by-step instructions 
 *************************
 Follow these step-by-step instructions to familiarise yourself with the flow of the web interface.
@@ -41,66 +39,27 @@ Follow these step-by-step instructions to familiarise yourself with the flow of
    :width: 95%
    :align: center
 
-**Step 2.** Select **Data for Mouse Lungs** from the search results. Click on scaffold icon. 
+**Step 2.** Select **Data for Mouse Lungs** from the search results. Click on |scaffold-map-icon| icon. 
 
 .. figure:: _images/lungs_02.png
    :figwidth: 95%
    :width: 95%
    :align: center
 
-**Step 3.** Click on the left and right lungs to highlight them in **green**.
+**Step 3.**  Allow model to load.
 
 .. figure:: _images/lungs_03.png
    :figwidth: 95%
    :width: 95%
    :align: center
 
-**Step 4.** Click on |open-control| icon to pop-up the drop-down menu.
+**Step 4.** Click on |open-control| icon for drop-down menu. Select only RML10x007 checkbox and zoom to view the confocal images in the right middle lobe(RML).
 
 .. figure:: _images/lungs_04.png
    :figwidth: 95%
    :width: 95%
    :align: center
 
-**Step 5.** Visibility can be turned ON or OFF for the items. 
-
-.. figure:: _images/lungs_05.png
-   :figwidth: 95%
-   :width: 95%
-   :align: center
-
-Working with the interface
-**************************
-This section explains how to use more specific features of the interface.
-
-: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`.
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diff --git a/source/MouseColon.rst b/source/MouseColon.rst
@@ -1,6 +1,7 @@
 Mapping Image Data in Mouse Colon
 =================================
-
+.. |scaffold-map-icon| image:: /_images/scaffold_map_icon.png					  
+						:width: 2 em
 .. contents:: Contents: 
    :local:
    :depth: 2
@@ -11,7 +12,6 @@ Overview
 
 A 3D scaffold fitted to the structural data of mouse colon is visualized in the webGL window. Apart from its 3D configuration, the scaffold is displayed as a flat preparation which represents the state where a colon is stretched out, cut open and laid flat on a surface for imaging purposes.  Segmented image data of enteric neurons and nerve fibers (Tache group) and vasculature (Howard group) of mouse tissue samples are mapped onto the flat scaffold based on the locations where the tissue samples were obtained from.  This allows image and experimental data to be embedded and displayed at labelled material points on the scaffold in both its 3D and flat configuration. The figure below illustrates an overview of the workflow.
 
-
 .. figure:: _images/colon_workflow.png
    :figwidth: 95%
    :width: 95%
@@ -23,98 +23,29 @@ Below is an **introductory video** which explains how the structural data of mou
 
      <iframe width="560" height="315" src="https://www.youtube.com/embed/gX2Njaqbk7U" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
 
-
-.. todo::
-    add link to final portal URL that takes user straight to this dataset display.
-
 Step-by-step instructions 
 *************************
 
-.. todo::
-	insert icon in step 2 and step 4
-
 Follow these step-by-step instructions to familiarise yourself with the flow of the web interface.
 
-
 **Step 1**. Click on the **Colon** on the flatmap to generate search results for colon. Alternatively, perform a search using keyword *colon* or *UBERON:0001155*.
 
 .. figure:: _images/colon_step1.png
    :figwidth: 95%
    :width: 95%
    :align: center
 
-**Step 2**. Select **Mouse Colon Data** from the search results. Click on the scaffold icon (insert icon).
+**Step 2**. Select **Mouse Colon Data** from the search results. Click on the scaffold icon (|scaffold-map-icon|).
 
 .. figure:: _images/colon_step2.png
    :figwidth: 95%
    :width: 95%
    :align: center
-
-.. todo::
-
-	this screenshot needs to be replaced after Hugh updates the interface to google map style.
-	Mabelle comments - I also asked Hugh to change “Mouse Colon MRI data” to “Mouse Colon MRI Data” instead)
 
 **Step 3**. Allow a few seconds for the scaffold to load. Navigate between the 3D and flat scaffold using the slider. Click on the **play** button to automate toggle between the two configurations. 
 
-.. todo::
-	this screenshot needs to be replaced after Alan updates the view and color.
-
 .. figure:: _images/colon_step3.png
    :figwidth: 95%
    :width: 95%
    :align: center
-
-**Step 4**. Control view of the scaffold with *left mouse* click to *rotate* the scaffold, *scroll mouse wheel* for *zoom*, and *right mouse* click to *pan*. Click on the control menu (Insert icon) to expand the controls menu. :guilabel:`Reset View` restores view of the scaffold to the default state. 
-
-.. figure:: _images/colon_step4.png
-   :figwidth: 95%
-   :width: 95%
-   :align: center
-
-**Step 5**. Uncheck the box next to the group name (for example, vessel) to hide the group from view.  Click on :guilabel:`View All` to return all groups to view within the window. 
-
-.. figure:: _images/colon_step5.png
-   :figwidth: 95%
-   :width: 95%
-   :align: center
-
-**Step 6**. Click on the group name under :guilabel:`Visibility Control` (for example, colon) to highlight the group green in the viewing window and to trigger a search request using the group name as a keyword. Click on :guilabel:`Close Controls` to close the expanded controls panel.
-
-.. figure:: _images/colon_step6.png
-   :figwidth: 95%
-   :width: 95%
-   :align: center   
-
-Alternatively, *hover* the mouse over the group (for example, colon) in the viewing window and click on the group when the group name appears to trigger a keyword search.  
-
-.. figure:: _images/colon_step6_1.png
-   :figwidth: 95%
-   :width: 95%
-   :align: center   	
-
-Working with the interface
-**************************
-This section explains how to use more specific features of the interface.
-
-: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`.
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diff --git a/source/RatSCG.rst b/source/RatSCG.rst
@@ -27,11 +27,6 @@ Knowledge that links the above pathways provides a key means to discover multipl
    :width: 95%
    :align: center
 
-.. todo::
-	This document guides a user of the SPARC Data Portal through the steps required to .......
-
-	Add link to final portal URL that takes user straight to this dataset display.
-
 Step-by-step instructions 
 *************************
 
@@ -71,47 +66,3 @@ Follow these step-by-step instructions to familiarise yourself with the flow of
    :figwidth: 95%
    :width: 95%
    :align: center
-
-Working with the interface
-**************************
-This section explains how to use more specific features of the interface.
-
-: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`.
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diff --git a/source/StellateGanglion.rst b/source/StellateGanglion.rst
@@ -2,8 +2,13 @@ Cell Body Segmentation and Electrophysiology Data: Stellate Ganglion
 ====================================================================
 
 .. |open-control| image:: /_images/open_control.png
-                      :width: 2 em			
-
+                      :width: 2 em	
+
+.. |scaffold-map-icon| image:: /_images/scaffold_map_icon.png					  
+						:width: 2 em	
+
+.. |data-icon| image:: /_images/data_icon.png					  
+						:width: 2 em
 .. contents:: Contents: 
    :local:
    :depth: 2
@@ -16,15 +21,12 @@ Mouse stellate ganglion neuronal cell shape data from the Shivkumar/Tompkins gro
 
 This document guides a user of the SPARC Data Portal through the steps required to discover a collection of segmented cell bodies from the stellate ganglion which have been mapped to a common coordinate framework for visualization purposes. The user is able to discover any electrophysiology data that has been recorded for each of the cell bodies.
 
-.. todo::
-    add link to final portal URL that takes user straight to this dataset display.
-
 Step-by-step instructions 
 *************************
 
 Follow these step-by-step instructions to familiarise yourself with the flow of the web interface.
 
-**Step 1**. Click on the **Stellate Ganglion** on the Flatmap.
+**Step 1**. Perform a search using keywords **stellate** or **stellate ganglion** and click on |scaffold-map-icon| icon.
 
 .. figure:: _images/sg_flatmap.png
    :figwidth: 95%
@@ -36,33 +38,23 @@ scaffold is a rectangular cube with slots to contain the stellate image stacks u
 the scaffold elements. Segmented cells (Soma) with associated axon and dendrites have been mapped and embedded in
 the image-scaffold structure. Each cell will have electro-physiological data properly registered.
 
-.. figure:: _images/stellate_scaffold_image01.png
-   :figwidth: 95%
-   :width: 95%
-   :align: center
-
-**Step 3**. In the current version, you would need to select the green circle from the search result to visualise the
-electro-physiological data associated with the samples.
-
-.. figure:: _images/use_case_2/Slide3.png
+.. figure:: _images/sg_snip1.png
    :figwidth: 95%
    :width: 95%
    :align: center
 
+**Step 3**. Click on |data-icon| icon on the search result to visualise the electro-physiological data associated with the samples.
 
-**Step 4**. The data is illustrated within a new tab called Data Viewer.
-
-.. figure:: _images/use_case_2/Slide1.PNG
+.. figure:: _images/sg_snip2.png
    :figwidth: 95%
    :width: 95%
    :align: center
 
 **Step 4**. Click on |open-control| to open the control panel. You can select different sweep or channel data for that cell in this tab to visualise at the same time.
 You can also export the data as a CSV format file.
 
-.. figure:: _images/use_case_2/Slide2.PNG
-   :figwidth: 80%
+.. figure:: _images/sg_snip3.png
+   :figwidth: 95%
    :width: 95%
    :align: center
 
-
diff --git a/source/_images/colon_step1.png b/source/_images/colon_step1.png
diff --git a/source/_images/colon_step2.png b/source/_images/colon_step2.png
diff --git a/source/_images/colon_step3.png b/source/_images/colon_step3.png
diff --git a/source/_images/data_icon.png b/source/_images/data_icon.png
diff --git a/source/_images/lungs_01.png b/source/_images/lungs_01.png
diff --git a/source/_images/lungs_02.png b/source/_images/lungs_02.png
diff --git a/source/_images/lungs_03.png b/source/_images/lungs_03.png
diff --git a/source/_images/lungs_04.png b/source/_images/lungs_04.png
diff --git a/source/_images/scaffold_map_icon.png b/source/_images/scaffold_map_icon.png
diff --git a/source/_images/sg_flatmap.png b/source/_images/sg_flatmap.png
diff --git a/source/_images/sg_snip1.png b/source/_images/sg_snip1.png
diff --git a/source/_images/sg_snip2.png b/source/_images/sg_snip2.png
diff --git a/source/_images/sg_snip3.png b/source/_images/sg_snip3.png
diff --git a/source/_images/sg_snip4.png b/source/_images/sg_snip4.png