Merge pull request #218 from mlin865/updateDoc

Update docs to list where data for scaffold came from

docs/scaffolds/bladder.rst

@@ -32,7 +32,7 @@ The bladder scaffold is provided with parameter sets for the following five spec
 * Pig
 * Rat
 
-These variants' geometry and annotations are best viewed in the **Scaffold Creator** tool in the ABI Mapping Tools. On the web, the latest published generic bladder scaffold variants can be viewed on the `SPARC Portal <https://sparc.science/>`_ by searching for ``bladder``, filtering for models, selecting a variant and viewing the scaffold in its Gallery tab.
+These variants' geometry and annotations are best viewed in the **Scaffold Creator** tool in the ABI Mapping Tools. On the web, the latest published generic bladder scaffold variants can be viewed on the `SPARC Portal <https://sparc.science/>`_ by searching for ``bladder``, filtering for anatomical models, selecting a variant and viewing the scaffold in its Gallery tab or via the `Organ Scaffolds <https://docs.sparc.science/docs/organ-scaffolds>`_ help article.
 
 The bladder scaffold script generates the scaffold mesh and geometry based on some parameters include the diameters for different axes, wall thickness, neck angle (for bladder only), etc., which are all defined for the bladder and urethra separately. The ability to control these parameters, as well as variations of them throughout the length of the bladder and urethra allows the scaffold to be configurable for different species and individuals.
 
@@ -42,6 +42,8 @@ Importantly, the entire scaffold is generated based on a configurable central pa
 
 Instructions for editing the central path are given with the ABI Mapping Tools **Scaffold Creator** documentation.
 
+The cat bladder scaffold is generated from images provided by Margot Damaser group from Cleveland Clinic. Tissue samples for three male and female rats were provided by Janet Keast et al. from the University of Melbourne for high-resolution microCT imaging. The structures and layers of interest from these images were then segmented using the MBF Tissue Mapper software to provide data for generating the geometry of the generic rat bladder scaffold. The human, mouse and pig bladder scaffolds are created based on images obtained from the literature.
+
 Coordinates
 -----------
 

docs/scaffolds/brainstem.rst

@@ -29,8 +29,9 @@ The brainstem scaffold is provided with parameter sets for the following six spe
 
 These variants' geometry and annotations are best viewed in the **Scaffold Creator** tool in the ABI Mapping Tools.
 On the web, the latest published generic brainstem scaffold variants can be viewed on the
-`SPARC Portal <https://sparc.science/>`_ by searching for ``brainstem``, filtering for models, selecting a variant and
-viewing the scaffold in its Gallery tab.
+`SPARC Portal <https://sparc.science/>`_ by searching for ``brainstem``, filtering for anatomical models, selecting a
+variant and viewing the scaffold in its Gallery tab or via the `Organ Scaffolds
+<https://docs.sparc.science/docs/organ-scaffolds>`_ help article.
 
 The brainstem scaffold script generates the scaffold mesh and geometry from a solid cylinder function based on a
 one dimensional central path with side axes controlling lateral dimensions. The parameters were carefully tuned for
@@ -41,6 +42,12 @@ Note that the D2 and D3 derivatives control the side dimensions, and derivatives
 of these along the central path. If editing, use the Interactive Functions to *Smooth derivatives*,
 *Make side derivatives normal* and *Smooth side cross derivatives* to make these as smooth as required.
 
+The generic brainstem scaffolds are fitted and smoothed to the segmentation data from a human (`BodyParts3D V4.3i
+<https://doi.org/10.1093/nar/gkn613>`_), a pig (Beckman Institute for Advanced Science and Technology, Pig Imaging Group,
+University Of Illinois Urbana-Champaign), a rat
+(`NeuroRat V4.0 <https://itis.swiss/virtual-population/animal-models/animals/neurorat/neurorat-v4/>`_), and a sheep
+(`Nitzsche et al. <https://doi.org/10.3389/fnana.2015.00069>`_).
+
 .. note::
 
    The central path is annotated with ``midbrain``, ``pons``, and ``medulla oblongata`` regions but these are only

docs/scaffolds/colon.rst

@@ -26,8 +26,9 @@ particular have different numbers of tenia coli:
 
 These variants' geometry and annotations are best viewed in the **Scaffold Creator** tool in the ABI Mapping Tools.
 On the web, the latest published generic colon scaffold variants can be viewed on the
-`SPARC Portal <https://sparc.science/>`_ by searching for ``colon``, filtering for models, selecting a variant and
-viewing the scaffold in its Gallery tab.
+`SPARC Portal <https://sparc.science/>`_ by searching for ``colon``, filtering for anatomical models, selecting a
+variant and viewing the scaffold in its Gallery tab or via the `Organ Scaffolds
+<https://docs.sparc.science/docs/organ-scaffolds>`_ help article.
 
 The colon scaffold script generates the scaffold mesh and geometry from an idealization of their cross-sectional profile
 shapes. The mesh is derived from ellipsoid and cubic functions based on a one dimensional central path which describes
@@ -39,6 +40,12 @@ Note that the D2 derivative along the path points towards the first node around
 If editing, use the Interactive Functions to *Smooth derivatives*, and *Smooth side cross derivatives* to make these as
 smooth as required.
 
+The central path used to generate the current mouse colon scaffold is obtained from tracing a central path from a
+dissection image obtained from the literature. Lixin Wang (UCLA), Yvette Tache (UCLA), and Marthe Howard
+(University of Toledo) provided lengths and diameter data for mouse colon. The pig colon scaffold is generated from
+images and measurements provided by Million Mulugeta, Muriel Larauche, and Yvette Tache (UCLA). The human colon scaffold
+is created based on average dimensions and images obtained from the literature.
+
 The mucosa, submucosa, circular muscle, longitudinal muscle and serosa layers of the colon are fully represented on
 the scaffold when *Number of elements through wall* is set to ``4``. Alternatively, the entire colon wall can be
 represented as a single layer by setting *Number of elements through wall* to ``1``.

docs/scaffolds/heart.rst

@@ -22,14 +22,16 @@ Variants
 The heart scaffold is provided with parameter sets for the following four species, which differ in shape, and in particular have different numbers of pulmonary veins:
 
 * Human (2 left, 2 right pulmonary veins)
+* Mouse (3 pulmonary veins: left, middle, right)
 * Pig (1 left, 1 right pulmonary veins)
 * Rat (3 pulmonary veins: left, middle, right)
-* Mouse (3 pulmonary veins: left, middle, right)
 
-These variants' geometry and annotations are best viewed in the **Scaffold Creator** tool in the ABI Mapping Tools. On the web, the latest published generic heart scaffold variants can be viewed on the `SPARC Portal <https://sparc.science/>`_ by searching for ``heart``, filtering for models, selecting a variant and viewing the scaffold in its Gallery tab. 
+These variants' geometry and annotations are best viewed in the **Scaffold Creator** tool in the ABI Mapping Tools. On the web, the latest published generic heart scaffold variants can be viewed on the `SPARC Portal <https://sparc.science/>`_ by searching for ``heart``, filtering for anatomical models, selecting a variant and viewing the scaffold in its Gallery tab or via the `Organ Scaffolds <https://docs.sparc.science/docs/organ-scaffolds>`_ help article.
 
 The heart scaffold script generates the scaffold mesh and geometry from ellipsoid and cubic functions with many parameters controlling the shape. The parameters were carefully tuned for each species, and it is not recommended that these be edited.
 
+The rat heart scaffold was calibrated using segmented image data from Clara Leung, Jack Zixi Cheng, Raj Vadigepalli, James Schwaber et al. (TJU, UCF), in `SPARC dataset <https://doi.org/10.26275/pb3l-251h>`_. Human and pig hearts were calibrated using data from the literature.
+
 An advanced optional feature is to check *Define epicardium layer* (set parameter to ``true``) which adds a layer of 3-D elements outside the myocardium to represent the thick epicardium layer consisting of epicardial fat and other tissue. This is currently only implemented over the atria, excluding the auricles.
 
 Coordinates

docs/scaffolds/lung.rst

@@ -30,19 +30,27 @@ The lung scaffold is provided with parameter sets for the following four species
 particular have different numbers of lobes:
 
 * Human (2 lobes in the left, 3 lobes in the right lung)
+* Mouse (1 lobe in the left, 4 lobes in the right lung)
 * Pig (2 lobes in the left, 4 lobes in the right lung)
 * Rat (1 lobe in the left, 4 lobes in the right lung)
-* Mouse (1 lobe in the left, 4 lobes in the right lung)
 
 These variants' geometry and annotations are best viewed in the **Scaffold Creator** tool in the ABI Mapping Tools.
 On the web, the latest published generic lung scaffold variants can be viewed on the
-`SPARC Portal <https://sparc.science/>`_ by searching for ``lung``, filtering for models, selecting a variant and
-viewing the scaffold in its Gallery tab.
+`SPARC Portal <https://sparc.science/>`_ by searching for ``lung``, filtering for anatomical models, selecting a variant
+and viewing the scaffold in its Gallery tab or via the `Organ Scaffolds
+<https://docs.sparc.science/docs/organ-scaffolds>`_ help article.
 
 The lung scaffold script generates the scaffold mesh and geometry from an idealization of their shapes. The left and
 right lung (excluding accessory lobe) are generated as half ellipsoids which are then reshaped by smooth functions for
 which parameters are provided on the scaffold, to give approximately realistic geometry for the species.
 The accessory lobe is similarly created as a triangular prism and reshaped.
+
+The generic lung scaffolds are parameterized and fitted to segmentation data from CT and MRI images from the following
+sources: human (`Osanlouy et al. <https://doi.org/10.1038/s41598-020-73117-w>`_), mouse
+(`Beichel et al. <https://lapdmouse.iibi.uiowa.edu/>`_), pig
+(`Lee et al. <https://doi.org/10.1152/japplphysiol.00868.2012>`_), rat
+(`NeuroRat V4.0 <https://itis.swiss/virtual-population/animal-models/animals/neurorat/neurorat-v4/>`_).
+
 [A special ``Material`` parameter set is provided to allow new species' parameters to be developed from the material
 coordinates definition (see below).]
 These parameters were carefully tuned for each species, and it is not recommended that these be edited.

docs/scaffolds/stomach.rst

@@ -26,8 +26,9 @@ The stomach scaffold is provided with parameter sets for the following four spec
 
 These variants' geometry and annotations are best viewed in the **Scaffold Creator** tool in the ABI Mapping Tools.
 On the web, the latest published generic stomach scaffold variants can be viewed on the
-`SPARC Portal <https://sparc.science/>`_ by searching for ``stomach``, filtering for models, selecting a variant and
-viewing the scaffold in its Gallery tab.
+`SPARC Portal <https://sparc.science/>`_ by searching for ``stomach``, filtering for anatomical models, selecting a
+variant and viewing the scaffold in its Gallery tab or via the `Organ Scaffolds
+<https://docs.sparc.science/docs/organ-scaffolds>`_ help article.
 
 The stomach scaffold script generates the scaffold mesh and geometry from an idealization of their shapes. The mesh is
 derived from ellipsoid and cubic functions based on a one dimensional central path with side axes controlling lateral
@@ -38,6 +39,10 @@ Note that the D2 and D3 derivatives control the side dimensions, and derivatives
 of these along the central path. If editing, use the Interactive Functions to *Smooth derivatives*,
 *Make side derivatives normal* and *Smooth side cross derivatives* to make these as smooth as required.
 
+The rat stomach scaffold is parameterized with average data from segmentation of Micro-CT image data of 11 animals
+performed at the Powley laboratory using Neurolucida (MBF Bioscience), while the human, mouse, and pig stomach scaffolds
+are parameterized with literature data to represent the anatomy accurately.
+
 The mucosa, submucosa, circular muscle, longitudinal muscle and serosa layers of the stomach are fully represented on
 the scaffold when *Number of elements through wall* is set to ``4``. Alternatively, the entire stomach wall can be
 represented as a single layer by setting *Number of elements through wall* to ``1``.