mouse-development-example.json

{

"header" : {
   "species": "mouse",
   "organ": "brain",
   "name" : "mouseDevelopmentalAtlas",

   "license" : "CC",
   "citation" : "doi:10.1016/j.neuroimage.2015.07.075",
   "version" : "1",
   "contact" : "mailto:jason.lerch@gmail.com",
   "comment" : "this is a mouse developmental atlas",
   "coordinate_system" : "self defined",
},

"datasource" : [
   {
      "id": "p01",
      "mimeType": "application/x-minc",
      "source": "file:///P01.mnc"
   },

   {
      "id": "p03",
      "mimeType": "application/x-minc",
      "source": "file:///P03.mnc",
   },

   {
      "@id": "p05",
      "mimeType": "application/x-minc-better-than-SPM",
      "source": "file:///P05.mnc",
   },

   {
      "@id": "p07",
      "mimeType": "application/x-minc-still-better-than-SPM",
      "source": "file:///P07.mnc",
   }
],

"structure" : [
   {
      "id": "hippocampus_l_p1",
      "sourceSelector" : {
         "data_key" : "12",
         "datasource" : "p01"},

      "annotation" : {
        "name": "left hippocampus p1",
        "shortName": "lHipP1",
        "seeAlso" : "hippocampus"},

      "renderOptions":{
         "color": "rgba(12,13,14,128)",
         "shininess": 0.5,}
   },

   {
      "id": "hippocampus_l_p3",
      "sourceSelector" : {
         "dataKey" : "12",
         "datasource" : "p03"},

      "annotation" : {
        "name": "left hippocampus p3",
        "shortName": "lHipP3",
        "seeAlso" : "hippocampus"},

      "renderOptions" : {
         "color": "rgba(12,14,14,128)",
         "shininess": 0.5},
   },

   {
      "id": "hippocampus_l_p5",
      "sourceSelector" : {
         "dataKey" : "12",
         "datasource" : "p05"},

      "annotation" : {
        "name": "left hippocampus p5",
        "shortName": "lHipP5",
        "seeAlso" : "hippocampus"},

      "renderOptions" : {
         "color": "rgba(12,15,14,128)",
         "shininess": 0.5},
   },

   {
      "id": "hippocampus_l_p7",
      "sourceSelector" : {
         "dataKey" : "12",
         "datasource" : "p07"},

      "annotation" : {
        "name": "left hippocampus p7",
        "shortName": "lHipP7",
        "seeAlso" : "hippocampus"},

      "renderOptions" : {
         "color": "rgba(12,16,14,128)",
         "shininess": 0.5},
   },
],

"groups" : [
   {
      "id" : "hippocampus",
      "annotation" : {
         "name": "hippocampus",
         "description": "it remembers stuff, don't cut it out.",
         "shortName": "Hip",
         "ontologyReferences": ["http://paxinos+watson.org/"]},

      "members" : ["hippocampus_l_p1", "hippocampus_l_p3", "hippocampus_l_p5", "hippocampus_l_p7"],
   }
]

}