Location: Generic human cecum scaffold @ c242cee65389 / OrganScaffold-settings.json

Author:
mlin865 <mlin865@aucklanduni.ac.nz>
Date:
2024-08-19 15:26:06+12:00
Desc:
Add organScaffold.exf and correct typo in README
Permanent Source URI:
https://models.physiomeproject.org/workspace/ba0/rawfile/c242cee65389980c6b23b53b36d1425ffbef1698/OrganScaffold-settings.json

{
    "scaffold_settings": {
        "deleteElementRanges": "",
        "displayAxes": false,
        "displayElementAxes": false,
        "displayElementNumbers": false,
        "displayLines": true,
        "displayLinesExterior": false,
        "displayMarkerPoints": false,
        "displayModelRadius": false,
        "displayNodeDerivativeLabels": [
            "D1"
        ],
        "displayNodeDerivativeVersion": 0,
        "displayNodeDerivatives": 0,
        "displayNodeNumbers": false,
        "displayNodePoints": false,
        "displaySurfaces": true,
        "displaySurfacesExterior": true,
        "displaySurfacesTranslucent": false,
        "displaySurfacesWireframe": false,
        "modelCoordinatesField": "coordinates",
        "scaffoldPackage": {
            "_ScaffoldPackage": true,
            "rotation": [
                0.0,
                0.0,
                0.0
            ],
            "scaffoldSettings": {
                "Base parameter set": "Human 2",
                "Circular muscle layer relative thickness": 0.25,
                "Corner outer radius factor": 0.536,
                "End tenia coli width": 10.0,
                "End tenia coli width derivative": 0.0,
                "Haustrum outer radius factor": 0.464,
                "Ileum wall thickness": 1.6,
                "Longitudinal muscle layer relative thickness": 0.05,
                "Mucosa relative thickness": 0.55,
                "Network layout": {
                    "_ScaffoldPackage": true,
                    "meshEdits": "EX Version: 3\nRegion: /\n!#nodeset nodes\nDefine node template: node1\nShape. Dimension=0\n#Fields=1\n1) coordinates, coordinate, rectangular cartesian, real, #Components=3\n x. #Values=6 (value,d/ds1,d/ds2,d2/ds1ds2,d/ds3,d2/ds1ds3)\n y. #Values=6 (value,d/ds1,d/ds2,d2/ds1ds2,d/ds3,d2/ds1ds3)\n z. #Values=6 (value,d/ds1,d/ds2,d2/ds1ds2,d/ds3,d2/ds1ds3)\nNode template: node1\nNode: 1\n -6.063000000000000e+01 -6.170000000000000e+00  2.660000000000000e+00  2.380000000000000e+00  3.310000000000000e+00  2.380000000000000e+00\n -8.053000000000000e+01 -1.010000000000000e+01  7.300000000000000e-01  9.900000000000000e-01 -2.970000000000000e+00  9.900000000000000e-01\n  8.952500000000000e+02 -5.870000000000000e+00 -4.050000000000000e+00 -1.140000000000000e+00  1.640000000000000e+00 -1.140000000000000e+00\nNode: 2\n -6.864000000000000e+01 -9.850000000000000e+00  3.880000000000000e+00  2.380000000000000e+00  2.820000000000000e+00  2.380000000000000e+00\n -9.329000000000001e+01 -1.542000000000000e+01  1.200000000000000e+00  9.900000000000000e-01 -2.460000000000000e+00  9.900000000000000e-01\n  8.880599999999999e+02 -8.510000000000000e+00 -6.660000000000000e+00 -1.140000000000000e+00  1.200000000000000e+00 -1.140000000000000e+00\nDefine node template: node2\nShape. Dimension=0\n#Fields=1\n1) coordinates, coordinate, rectangular cartesian, real, #Components=3\n x. #Values=11 (value,d/ds1(2),d/ds2(2),d2/ds1ds2(2),d/ds3(2),d2/ds1ds3(2))\n y. #Values=11 (value,d/ds1(2),d/ds2(2),d2/ds1ds2(2),d/ds3(2),d2/ds1ds3(2))\n z. #Values=11 (value,d/ds1(2),d/ds2(2),d2/ds1ds2(2),d/ds3(2),d2/ds1ds3(2))\nNode template: node2\nNode: 3\n -8.039000000000000e+01 -7.790000000000000e+00 -1.365000000000000e+01  2.072000000000000e+01  5.590000000000000e+00  2.380000000000000e+00  2.380000000000000e+00  2.470000000000000e+00  1.510000000000000e+00  2.380000000000000e+00  2.380000000000000e+00\n -1.113700000000000e+02 -9.800000000000000e-01 -2.074000000000000e+01 -4.040000000000000e+00  1.310000000000000e+00  9.900000000000000e-01  9.900000000000000e-01  2.383000000000000e+01 -1.370000000000000e+00  9.900000000000000e-01  9.900000000000000e-01\n  8.782900000000000e+02  1.236000000000000e+01 -1.103000000000000e+01  1.254000000000000e+01 -9.380000000000001e+00 -1.140000000000000e+00 -1.140000000000000e+00  3.610000000000000e+00  7.100000000000000e-01 -1.140000000000000e+00 -1.140000000000000e+00\nNode template: node1\nNode: 4\n -7.169000000000000e+01 -9.550000000000001e+00  1.741000000000000e+01  3.730000000000000e+00  8.200000000000000e-01  3.740000000000000e+00\n -1.090000000000000e+02 -3.730000000000000e+00 -4.850000000000000e+00  6.800000000000000e-01  1.994000000000000e+01  6.899999999999999e-01\n  8.660400000000000e+02  1.206000000000000e+01  1.146000000000000e+01  4.200000000000000e+00  7.200000000000000e+00  4.200000000000000e+00\nNode: 5\n -8.720999999999999e+01 -4.750000000000000e+00  2.327000000000000e+01  2.460000000000000e+00  3.090000000000000e+00  1.830000000000000e+00\n -1.110600000000000e+02  4.100000000000000e-01 -3.130000000000000e+00 -3.900000000000000e-01  2.446000000000000e+01  4.600000000000000e-01\n  8.905400000000000e+02  1.239000000000000e+01  7.880000000000000e+00 -2.950000000000000e+00  4.500000000000000e-01 -4.310000000000000e+00\nGroup name: meshEdits\n!#nodeset nodes\nNode group:\n1..5\n",
                    "rotation": [
                        0.0,
                        0.0,
                        0.0
                    ],
                    "scaffoldSettings": {
                        "Base parameter set": "Default",
                        "Define inner coordinates": false,
                        "Structure": "1-2-3.2, 4-3-5"
                    },
                    "scaffoldTypeName": "1D Network Layout 1",
                    "scale": [
                        1.0,
                        1.0,
                        1.0
                    ],
                    "translation": [
                        0.0,
                        0.0,
                        0.0
                    ],
                    "userAnnotationGroups": [
                        {
                            "_AnnotationGroup": true,
                            "dimension": 1,
                            "identifierRanges": "1-4",
                            "name": "caecum",
                            "ontId": "UBERON:0001153"
                        },
                        {
                            "_AnnotationGroup": true,
                            "dimension": 1,
                            "identifierRanges": "1-2",
                            "name": "ileum part of cecum",
                            "ontId": "None"
                        }
                    ]
                },
                "Number of elements along segment": 12,
                "Number of elements around haustrum": 8,
                "Number of elements around tenia coli": 2,
                "Number of elements through wall": 1,
                "Number of segments": 1,
                "Number of tenia coli": 3,
                "Refine": false,
                "Refine number of elements along": 1,
                "Refine number of elements around": 1,
                "Refine number of elements through wall": 1,
                "Segment length end derivative factor": 0.5,
                "Segment length mid derivative factor": 3.0,
                "Start tenia coli width": 10.0,
                "Start tenia coli width derivative": 0.0,
                "Submucosa relative thickness": 0.15,
                "Tenia coli thickness": 1.6,
                "Use cross derivatives": false,
                "Use linear through wall": true,
                "Wall thickness": 1.6
            },
            "scaffoldTypeName": "3D Cecum 1",
            "scale": [
                1.0,
                1.0,
                1.0
            ],
            "translation": [
                0.0,
                0.0,
                0.0
            ]
        }
    },
    "segmentation_data_settings": {
        "displayDataContours": true,
        "displayDataMarkerNames": true,
        "displayDataMarkerPoints": true,
        "displayDataPoints": false,
        "displayDataRadius": false
    }
}