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Updated documentation to address original use-case overview proposed by Peter
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shsa992 committed Aug 22, 2019
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2 changes: 1 addition & 1 deletion source/DataViewer.rst
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Expand Up @@ -52,7 +52,7 @@ This mode is used to navigate larger datasets. It has search capability to plot
Interactive Graphics Controls
*****************************

You can refine the view by draging over a region of interest.
You can refine the view by dragging over a region of interest.

.. figure:: _images/plot_refine.jpg
:figwidth: 95%
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43 changes: 20 additions & 23 deletions source/MouseBrainStemLungs.rst
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Expand Up @@ -14,52 +14,49 @@ Mapping Gene Expression in the Mouse Lungs from Images to Scaffold
Overview
********

A 3D scaffold of the mouse thoracic cavity created using segmentation of longitudinal microCT scans from the SIMBA VIA (Vision and Image Analysis) public database is visualized in the webGL window. The trachea and main bronchi are also shown as rings of segmented points. Confocal stained images from Taylor-Clark group for mouse lungs are embedded into the scaffold. The confocal images were obtained from the right middle lobe (RML). The scaffold was registered to ensure alignment with the airway branch visible on the confocal. This use-case will be the first of many that link the organ systems with the brain stem.

.. figure:: _images/use_case5_lung.png
:figwidth: 100%
:width: 91%
:align: center

Below is an **introductory video** which explains how an anatomically based 3D thoracic shape of the lungs are generated.

.. raw:: html

<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>

A 3D scaffold of the mouse thoracic cavity created using segmentation of longitudinal microCT scans from the SIMBA VIA (Vision and Image Analysis) public database is visualized. The trachea and main bronchi are also shown as rings of segmented points. Confocal stained images from Taylor-Clark group for mouse lungs are embedded into the scaffold. The confocal images were obtained from the right middle lobe (RML). The scaffold was registered to ensure alignment with the airway branch visible on the confocal. This use-case is one of many that link an organ systems with the brainstem.

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 **Lungs** on the flatmap to generate search results for lungs.

.. figure:: _images/lungs_01.png
:figwidth: 95%
:width: 95%
:align: center

**Step 2.** Select **Data for Mouse Lungs** from the search results. Click on |scaffold-map-icon| icon.
**Step 1**. The default **Result** column displays the use cases available on the portal. Click on the
*Mapping Gene Expression in the Mouse Lungs from Images to Scaffold* box, then on |scaffold-map-icon| icon.

.. figure:: _images/lungs_02.png
:figwidth: 95%
:width: 95%
:align: center

**Step 3.** Allow model to load.
**Step 2.** Allow model to load.

.. figure:: _images/lungs_03.png
:figwidth: 95%
:width: 95%
:align: center

**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).
**Step 3.** To view only the confocal image in the right middle lobe (RML), select only RML10x007 checkbox after clicking on |open-control| icon for drop-down menu.

.. figure:: _images/lungs_04.png
:figwidth: 95%
:width: 95%
:align: center

Scaffold Generation
*************************

A diagram and video are below, detailing the workflow for the generation of an anatomically-based 3D thoracic shape of the lungs.

.. figure:: _images/use_case5_lung.png
:figwidth: 100%
:width: 91%
:align: center

.. raw:: html

<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>





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41 changes: 20 additions & 21 deletions source/MouseColon.rst
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Expand Up @@ -10,42 +10,41 @@ Mapping Image Data in Mouse Colon
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%
:align: center

Below is an **introductory video** which explains how the structural data of mouse colon are mapped onto a 3D scaffold.

.. raw:: html

<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>
A 3D scaffold fitted to the structural data of mouse colon is visualized. 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.

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 **Colon** on the flatmap to generate search results for colon. Alternatively, perform a search using keyword *colon* or *UBERON:0001155*.
**Step 1**. The default **Result** column displays the use cases available on the portal. Click on the
*Mapping Image Data in Mouse Colon* box. Click on the scaffold icon (|scaffold-icon|). Click on the scaffold icon (|scaffold-map-icon|).

.. figure:: _images/colon_step1.png
.. figure:: _images/colon_step2.png
:figwidth: 95%
:width: 95%
:align: center
**Step 2**. Select **Mouse Colon Data** from the search results. Click on the scaffold icon (|scaffold-map-icon|).
**Step 2**. 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.

.. figure:: _images/colon_step2.png
.. figure:: _images/colon_step3.png
:figwidth: 95%
:width: 95%
:align: center

**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.


.. figure:: _images/colon_step3.png
Scaffold Generation
*************************

The Figure below illustrates an overview of the workflow.

.. figure:: _images/colon_workflow.png
:figwidth: 95%
:width: 95%
:align: center


Below is an **introductory video** which explains how the structural data of mouse colon are mapped onto a 3D scaffold.

.. raw:: html

<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>
33 changes: 17 additions & 16 deletions source/MouseHeart.rst
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Expand Up @@ -15,38 +15,26 @@ Mapping the Mouse Heart Neurites from Image to Scaffold
Overview
********

Mouse heart immunohistochemical mapping of neural pathways in cleared heart (sham heart 4) stained with PGP9.5
Immunohistochemical mapping of neural pathways in cleared heart (sham heart 4) stained with PGP9.5
(glycoprotein surface axonal antibody labelling) from the Shivkumar/Pradeep group is displayed in a 3D mouse heart
scaffold that has been fitted to the segmented heart surface data from Sham Heart 44, which provides a more extensive
geometric dataset. Future experiments are likely to provide much better quality mouse data for both the heart's anatomy
and its embedded neurons. Figure 1 illustrates an overview of the workflow.

.. figure:: _images/use_case3_workflow_white.png
:figwidth: 95%
:width: 95%
:align: center

Below is an **introductory video** which explains the mapping of the mouse heart neurites from image to scaffold.

.. 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>

and its embedded neurons.

Step-by-step instructions
*************************

Follow these step-by-step instructions to familiarise yourself with the flow of the web interface.

**Step 1**. The default **Result** column displays some of the use cases available on the portal. Click on
**Step 1**. The default **Result** column displays the use cases available on the portal. Click on the
*Mapping the Mouse Heart Neurites from Image to Scaffold* box.

.. figure:: _images/use_case_3/Slide1.PNG
:figwidth: 95%
:width: 85%
:align: center

**Step 2** Now click on the |scaffold-icon| to open the **Scaffold Viewer** tab to visualise the heart scaffold.
**Step 2** Click on the |scaffold-icon| to open the **Scaffold Viewer** tab to visualise the heart scaffold.

.. figure:: _images/use_case_3/Slide2.PNG
:figwidth: 95%
Expand Down Expand Up @@ -83,5 +71,18 @@ surface.
:width: 85%
:align: center

Scaffold Generation
*************************

The following figure illustrates an overview of the workflow for the generation of the 3D scaffold.

.. figure:: _images/use_case3_workflow_white.png
:figwidth: 95%
:width: 95%
:align: center

Below is an **introductory video** which explains the mapping of the mouse heart neurites from image to scaffold.

.. 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>
27 changes: 20 additions & 7 deletions source/PigHeart.rst
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Expand Up @@ -32,7 +32,7 @@ Step-by-step instructions

Follow these step-by-step instructions to familiarise yourself with the flow of the web interface.

**Step 1:** The default **Result** column displays some of the use cases available on the portal. Click on
**Step 1:** The default **Result** column displays some of the use cases available on the portal. Click on the
*Mapping Cardiac Electromechanics in the Pig* box.

.. figure:: _images/pig_slide1.png
Expand All @@ -59,20 +59,33 @@ Press **play** to see the video.
:width: 90%
:align: center

**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

**Step 5:** By clicking on |open-control| you can control visibility of each of the graphical objects in the scene.
**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


Scaffold Generation
*************************

The following Figure depicts the workflow for the generation of the 3D scaffold.

.. figure:: _images/pig_workflow.png
:figwidth: 95%
:width: 90%
:align: center


Future Steps
*************************
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.
52 changes: 26 additions & 26 deletions source/RatHeart.rst
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Expand Up @@ -15,64 +15,50 @@ Mapping Cellular Gene Expression in the Rat Heart from Image to Scaffold
Overview
********

Rat heart geometric `3Scan <www.3scan.com>`_ data for both ventricles and both atria from the Schwaber/Vadigepalli/Cheng group has been fitted with a 3D rat heart scaffold.
The location of a cluster of 151 ICN cell samples, which have been lifted for RNA-Seq analysis (molecular cell body transcript data) from a region of the left atrium (from a different animal), are indicated on the 3D scaffold.
Rat heart geometric `3Scan <https://www.3scan.com>`_ data for both ventricles and both atria from the Schwaber/Vadigepalli/Cheng group has been fitted with a 3D rat heart scaffold.
The location of a cluster of 151 intrinsic cardiac neuron (ICN) samples, which have been lifted for RNA-Seq analysis (molecular cell body transcript data) from a region of the left atrium (from a different animal), are indicated on the 3D scaffold.
To click on one of these tissue locations displays the RNA message level for the 154 genes examined.
To visualize the spatial distribution of the RNA message, the 151 samples have been fitted with a continuous field description using scaffold nodal parameters.
Any one of the 154 genes can be selected to show the spatial variation of that transcript as a heat map.
Rat heart neural pathway data showing the efferent connectome linking ICN cells in the left atrium and the SA node cells on the right atrium are visualized in the next iteration of this use case.

**Note:** the treatment process needed to extract the cells for RNA-Seq analysis left that rat heart in a very distorted state and was therefore not fitted with a scaffold.
Instead, corresponding locations of the ICN cells in the much less distorted 3Scan-processed heart were identified by eye and the cell information was transferred to that heart.

.. figure:: _images/use_case4_workflow_white.png
:figwidth: 95%
:width: 90%
:align: center

Step-by-step instructions
*************************

Follow these step-by-step instructions to familiarize yourself with the flow of the Web interface.

**Step 1**. Click on the Heart on the flatmap to generate search results for heart, i.e. `UBERON:948 <http://purl.obolibrary.org/obo/UBERON_0000948>`_.

.. figure:: _images/use_case_4/Step1.png
:figwidth: 95%
:width: 72%
:align: center

**Step 2**. Click on the |scaffold-map-icon| icon.
**Step 1**. The default **Result** column displays the use cases available on the portal. Click on the
*Mapping Cellular Gene Expression in the Rat Heart from Image to Scaffold* box, then click on |scaffold-map-icon| icon.

.. figure:: _images/use_case_4/Step2.png
:figwidth: 95%
:width: 72%
:align: center

**Step 3**. The Scaffold Viewer tab opens and the fitted heart scaffold can be visualized.
The Scaffold Viewer tab opens and the fitted heart scaffold can be visualized.
A number of lifted neuronal cells have been mapped and registered on the scaffold (purple spheres).

.. figure:: _images/use_case_4/Step3.png
:figwidth: 95%
:width: 72%
:align: center

**Step 4**. Click on the |open-control| icon to pop up the drop-down menu.
**Step 2**. Click on the |open-control| icon to pop up the drop-down menu.
Visibility can be turned *on* or *off* for each item.

.. figure:: _images/use_case_4/Step4.png
:figwidth: 95%
:width: 72%
:align: center

**Step 5**. Hover on the different regions to highlight the chambers separately.
**Step 3**. Hover on the different regions to highlight the chambers separately.

.. figure:: _images/use_case_4/Step5.png
:figwidth: 95%
:width: 72%
:align: center

**Step 6**. Each cell has been lifted and assayed for the expression of 154 genes selected as associated with neuromodulation and cardiac function using qPCR or RNASeq.
Each cell has been lifted and assayed for the expression of 154 genes selected as associated with neuromodulation and cardiac function using qPCR or RNASeq.
These have been mapped on the registered cells on the scaffold.
Each cell has a unique ID.

Expand All @@ -81,14 +67,14 @@ Each cell has a unique ID.
:width: 72%
:align: center

**Step 7**. Now, click on the |data-icon| icon.
**Step 4**. Now, click on the |data-icon| icon.

.. figure:: _images/use_case_4/Step7.png
:figwidth: 95%
:width: 72%
:align: center

**Step 8**. The Data Viewer tab opens to view the gene expression data.
The Data Viewer tab opens to view the gene expression data.
At this point, the data can only viewed using a bar chart.
However, additional visualization capabilities, such as heatmap and clustering, will be available in the future.

Expand All @@ -97,18 +83,32 @@ However, additional visualization capabilities, such as heatmap and clustering,
:width: 72%
:align: center

**Step 9**. From the drop-down menu, more genes can be added to the bar chart.
**Step 5**. Add more genes to the bar chart by expanding the drop-down menu.

.. figure:: _images/use_case_4/Step9.png
:figwidth: 95%
:width: 72%
:align: center

**Step 10**. The bar chart will show the expression of each gene using a unique color for all the registered cells on the scaffold.
The bar chart will show the expression of each gene using a unique color for all the registered cells on the scaffold.

.. figure:: _images/use_case_4/Step10.png
:figwidth: 95%
:width: 72%
:align: center


Scaffold Generation
*************************

The following Figure depicts the workflow for the generation of the 3D scaffold.

.. figure:: _images/use_case4_workflow_white.png
:figwidth: 95%
:width: 90%
:align: center

The treatment process needed to extract the cells for RNA-Seq analysis left that rat heart in a very distorted state and was therefore not fitted with a scaffold.
Instead, corresponding locations of the ICN cells in the much less distorted 3Scan-processed heart were identified by eye and the cell information was transferred to that heart.


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