Multi-scale, multi-organ, multi-species SPARC map management
FOCUS: Tools and Technologies
PRINCIPAL INVESTIGATOR(S): Peter Hunter
INSTITUTION(S): University of Auckland
FUNDING PROGRAM(S): SPARC
NIH AWARD: OT3OD025349
The aim of this project is to provide tools for visualising data and models generated by the SPARC (Stimulating Peripheral Activity to Relieve Conditions) consortium, which is generating data and models associated with the autonomic nervous system. By mapping the paths of these nerves throughout the body and understanding their role in controlling organ function, the NIH funded program will help provide the means for medical device companies to develop new stimulators that can modulate organ function in order to improve physiological function and hence relieve a medical condition. The MAP-CORE is one of three components of the Data and Resource Centre (DRC) for SPARC. DAT- CORE will manage the actual data generated by the SPARC community. MAP-CORE will integrate the multiple types of data (also from multiple species) into a cohesive whole, and organise and display it in a way that is useful to both the SPARC science community and the medical device companies. SIM-CORE will develop a framework, including simulation tools, to connect mathematical models of neural and other physiological activity based on the SPARC data. The MAP-CORE will ensure that suitable community standards such as CellML, SBML, FieldML and SED-ML are used (and if necessary, further developed) for encoding and annotating the data, models and simulations to ensure reproducibility, and to help ensure that all data and models are appropriately annotated to make them findable and accessible by the community in the DAT-CORE database. MAP-CORE will use ApiNATOMY to provide annotations for biological context and a framework for implementing biophysical concepts such as conservation of mass and conservation of energy. A portal, based on web 2.0 and subsequent standards, will be developed that brings the anatomy and multiscale physiology of all organ systems into a single database-driven user interface. The user will be able to examine data and models at all scales and to generate predictive multiscale models (solved with the SIM-CORE tools) to answer specific questions associated with the autonomic control of the visceral organs.
Associated Content
Generic rat heart scaffold
Annotated heart scaffold for rat available for registration of segmented neural anatomical-functional mapping of cardiac neural circuits.
Generic pig colon scaffold
Annotated pig colon scaffold available for registration of segmented neural anatomical-functional mapping of enteric neural circuits.
Generic human colon scaffold
Annotated human colon scaffold available for registration of segmented neural anatomical-functional mapping of enteric neural circuits.
Generic cat bladder scaffold
Annotated bladder scaffold for cat available for registration of segmented neural anatomical-functional mapping of LUT neural circuits.
Generic mouse colon scaffold
Annotated mouse colon scaffold available for registration of segmented neural anatomical-functional mapping of enteric neural circuits.
Generic mouse small intestine scaffold
Annotated mouse small intestine scaffold available for registration of segmented neural anatomical-functional mapping of enteric neural circuits.
Generic human small intestine scaffold
Annotated human small intestine scaffold available for registration of segmented neural anatomical-functional mapping of enteric neural circuits.
Generic human gastrointestinal tract scaffold
Annotated human gastrointestinal tract scaffold available for registration of segmented neural anatomical-functional mapping of enteric neural circuits.
Generic human cecum scaffold
Annotated human cecum scaffold available for registration of segmented neural anatomical-functional mapping of enteric neural circuits.
Scaffold map - Integrated mapping of rat stomach data
Axon innervation, vasculature and cell density data from different experiments are mapped onto a common coordinate framework provided by the generic rat stomach scaffold.
Scaffold map - Anterograde tracing of spinal afferent innervation in flat-mounts of the rat stomach
Segmentation of axon innervation and its density field are mapped to a generic rat stomach scaffold for qualitative and quantitative visualisation and analysis.
Scaffold map - MicroCT imaging of rat stomach vasculature with Microfil MV-122
Stomach vasculature derived from microCT imaging of Microfil MV-122 perfusion is mapped to the rat stomach scaffold.
Scaffold map - Quantitative analysis of enteric neurons containing choline acetyltransferase and nitric oxide synthase immunoreactivities in the submucosal and myenteric plexuses of the porcine colon
Choline acetyltransferase and nitric oxide synthase immunoreactivities in the inner submucosal plexus of the ascending porcine colon are mapped onto the pig colon scaffold.
A 3D human whole-body model with integrated organs vasculature musculoskeletal and nervous systems for mapping nerves
The generated body scaffold was fitted to data, and the organ fiducial markers were embedded in the human whole-body. The landmarks were obtained from image data and also were defined in the body scaffold. Furthermore, nerve centrelines are added.
Scaffold map - Mapping of human gastric enteroendocrine cells
Distributions of enteroendocrine cells (EEC), defined by the hormones they contain within the human fundus and corpus are mapped onto the human stomach scaffold.
Scaffold map - Quantification of rat gastric enteroendocrine cells
Distributions of enteroendocrine cells (EEC), defined by the hormones they contain within the rat corpus and antrum are mapped onto the rat stomach scaffold.
Scaffold map - Influence of direct colon tissue electrical stimulation on colonic motility in anesthetized male Yucatan minipig
Time series manometry data derived from direct proximal colon, transverse colon and distal wall electrical stimulation in the original dataset are mapped onto the pig colon scaffold.
Generic human esophagus scaffold
Annotated human esophagus scaffold available for registration of segmented neural anatomical-functional mapping of enteric neural circuits.
Pig whole-body with embedded organs using automatic workflow for inserting the organs
This dataset includes lung and heart inserted into the pig whole-body using an automated workflow.
Generic pig stomach scaffold
Annotated pig stomach scaffold available for registration of segmented neural anatomical-functional mapping of enteric neural circuits.
Generic sheep brainstem scaffold
Annotated sheep brainstem scaffold available for registration of segmented neural anatomical-functional mapping of neural circuits.
Generic pig lung scaffold
Annotated lung scaffold for pig available for registration of segmented neural anatomical-functional mapping of pulmonary neural circuits.
Generic pig brainstem scaffold
Annotated brainstem scaffold for pig available for registration of segmented neural anatomical-functional mapping of neural circuits.
Rat whole-body with embedded organs using automatic workflow for inserting the organs
This dataset includes lung, bladder, heart, stomach and brainstem inserted into the rat whole-body using an automated workflow.
Human whole-body with embedded organs using automatic workflow for inserting the organs
This dataset includes lung, bladder, heart, stomach and brainstem inserted into the human whole-body using an automated workflow.
Generic mouse brainstem scaffold
Annotated mouse brainstem scaffold available for registration of segmented neural anatomical-functional mapping of neural circuits.
Generic mouse heart scaffold
Annotated heart scaffold for mouse available for registration of segmented neural anatomical-functional mapping of cardiac neural circuits.
Generic pig bladder scaffold
Annotated bladder scaffold for pig available for registration of segmented neural anatomical-functional mapping of lower urinary tract (LUT) neural circuit.
Generic mouse bladder scaffold
Annotated bladder scaffold for mouse available for registration of segmented neural anatomical-functional mapping of lower urinary tract (LUT) neural circuits.
Mouse whole-body with embedded organs
The generated body scaffold was fitted to data and the organ fiducial markers were embedded in the mouse whole-body. The landmarks were obtained from segmenting MRI data and also were defined in the body scaffold.
Generic mouse stomach scaffold
Annotated mouse stomach scaffold available for registration of segmented neural anatomical-functional mapping of enteric neural circuits.
Fabbri-based composite SAN model
CellML version of the Fabbri et al. 2017 human sinoatrial node (SAN) cell model and an ODE-based version of the Gerstner & Kistler 2002 brain stem model combined to demonstrate the effect of brain stem activity on heart rate
Human whole-body with embedded organs
The generated body scaffold was fitted to data, and the organ fiducial markers were embedded in the human whole-body. The landmarks were obtained from image data and also were defined in the body scaffold. Furthermore, the nerves centrelines are added.
Generic rat brainstem scaffold
Annotated rat brainstem scaffold available for registration of segmented neural anatomical-functional mapping of neural circuits.
Generic human brainstem scaffold
Annotated human brainstem scaffold available for registration of segmented neural anatomical-functional mapping of neural circuits.
Rat whole-body with embedded organs
The generated body scaffold was fitted to data and the organ fiducial markers were embedded in the rat whole-body. The landmarks were obtained from image data and also were defined in the body scaffold.
Generic rat lung scaffold
Annotated lung scaffold for rat available for registration of segmented neural anatomical-functional mapping of pulmonary neural circuits.
Generic human bladder scaffold
Annotated bladder scaffold for human available for registration of segmented neural anatomical-functional mapping of LUT neural circuits.
Generic human stomach scaffold
Annotated human stomach scaffold available for registration of segmented neural anatomical-functional mapping of enteric neural circuits.
Computational analysis of the human sinus node action potential - Model development and effects of mutations
CellML version of the Fabbri et al. 2017 mathematical model of the spontaneous electrical activity of a human sinoatrial node (SAN) pacemaker cell
Human whole-body scaffold
Annotated human whole-body scaffold (abdomen, diaphragm, thorax, neck, head, skin, spinal cord) with embedded vagus nerves.
Rat whole-body scaffold
Annotated rat whole body scaffold (abdomen, diaphragm, thorax, neck, head, skin, spinal cord) with embedded vagus nerves.
Generic rat stomach scaffold
Annotated rat stomach scaffold available for registration of segmented neural anatomical-functional mapping of enteric neural circuits.
Generic rat bladder scaffold
Annotated bladder scaffold for rat available for registration of segmented neural anatomical-functional mapping of LUT neural circuits.
Generic human lung scaffold
Annotated lung scaffold for human available for registration of segmented neural anatomical-functional mapping of pulmonary neural circuits.
Generic pig heart scaffold
Annotated heart scaffold for pig available for registration of segmented neural anatomical-functional mapping of cardiac neural circuits.
Generic mouse lung scaffold
Annotated lung scaffold for mouse available for registration of segmented neural anatomical-functional mapping of pulmonary neural circuits.
Generic human heart scaffold
Annotated heart scaffold for human available for registration of segmented neural anatomical-functional mapping of cardiac neural circuits.
