Displaying non-atlas volumes

Warning

This section is still been developed, and the content/API may change in future versions.

Interactive atlas can allow for arbitary volumes to be viewed, either in the context of a reference template or without.

Viewing standalone volumes

standaloneVolumes query param is parsed, and parsed as JSON. They are passed directly to be rendered in nehuba.

If both standaloneVolumes and templateSelected are present, the latter is ignored.

Query param

standaloneVolumes

Example

/?standaloneVolumes=%5B%22nifti%3A%2F%2Fhttp%3A%2F%2Flocalhost%3A1234%2Fnii.gz%22%2C%22precomputed%3A%2F%2Fhttp%3A%2F%2Flocalhost%3A4321%2Fvolume%22%5D

decoding and parsing as JSON:

[
  "nifti://http://localhost:1234/nii.gz",
  "precomputed://http://localhost:4321/volume"
]

Viewing registered volumes

previewingDatasetFiles query param is parsed, and parsed as JSON. Then, relevant volume information is retrieved, and displayed with templateSelected and parcellationSelected

Query param

previewingDatasetFiles

Example

/?templateSelected=Big+Brain+%28Histology%29&parcellationSelected=Grey%2FWhite+matter&previewingDatasetFiles=%5B%7B%22datasetId%22%3A%22minds%2Fcore%2Fdataset%2Fv1.0.0%2Fb08a7dbc-7c75-4ce7-905b-690b2b1e8957%22%2C%22filename%22%3A%22Overlay%20of%20data%20modalities%22%7D%5D

decoding and parsing as JSON:

[
  {
    "datasetId":"minds/core/dataset/v1.0.0/b08a7dbc-7c75-4ce7-905b-690b2b1e8957",
    "filename":"Overlay of data modalities"
  }
]

The metadata fetched from these ID ¹ is as follows.

{
  "name": "Overlay of data modalities",
  "filename": "Overlay of data modalities",
  "mimetype": "application/json",
  "data": {
    "iav-registered-volumes": {
      "volumes": [
        {
          "name": "PLI Fiber Orientation Red Channel",
          "source": "precomputed://https://zam10143.zam.kfa-juelich.de/chumni/nifti/8b970e20de0e31b1b78ec9dba13d20319111189711983cb03ddbb7cc/BI-FOM-HSV_R",
          "shader": "void main(){ float x = toNormalized(getDataValue()); if (x < 0.1) { emitTransparent(); } else { emitRGB(vec3(1.0 * x, x * 0., 0. * x )); } }",
          "transform": [[0.7400000095367432, 0, 0, 11020745], [0, 0.2653011679649353, -0.6908077001571655, 2533286.5], [0, 0.6908077001571655, 0.2653011679649353, -32682974], [0, 0, 0, 1]],
          "opacity": 1.0
        },
        {
          "name": "PLI Fiber Orientation Green Channel",
          "source": "precomputed://https://zam10143.zam.kfa-juelich.de/chumni/nifti/8b970e20de0e31b1b78ec9dba13d20319111189711983cb03ddbb7cc/BI-FOM-HSV_G",
          "shader": "void main(){ float x = toNormalized(getDataValue()); if (x < 0.1) { emitTransparent(); } else { emitRGB(vec3(0. * x, x * 1., 0. * x )); } }",
          "transform": [[0.7400000095367432, 0, 0, 11020745], [0, 0.2653011679649353, -0.6908077001571655, 2533286.5], [0, 0.6908077001571655, 0.2653011679649353, -32682974], [0, 0, 0, 1]],
          "opacity": 0.5
        },
        {
          "name": "PLI Fiber Orientation Blue Channel",
          "source": "precomputed://https://zam10143.zam.kfa-juelich.de/chumni/nifti/8b970e20de0e31b1b78ec9dba13d20319111189711983cb03ddbb7cc/BI-FOM-HSV_B",
          "shader": "void main(){ float x = toNormalized(getDataValue()); if (x < 0.1) { emitTransparent(); } else { emitRGB(vec3(0. * x, x * 0., 1.0 * x )); } }",
          "transform": [[0.7400000095367432, 0, 0, 11020745], [0, 0.2653011679649353, -0.6908077001571655, 2533286.5], [0, 0.6908077001571655, 0.2653011679649353, -32682974], [0, 0, 0, 1]],
          "opacity": 0.25
        },
        {
          "name": "Blockface Image",
          "source": "precomputed://https://zam10143.zam.kfa-juelich.de/chumni/nifti/cb905d54437734b39807e252ef8aa68bc6ac889047fbebbafd885490/BI",
          "shader": "void main(){ float x = toNormalized(getDataValue()); if (x < 0.1) { emitTransparent(); } else { emitRGB(vec3(0.8 * x, x * 1., 0.8 * x )); } }",
          "transform": [[0.7400000095367432, 0, 0, 11020745], [0, 0.2653011679649353, -0.6908077001571655, 2533286.5], [0, 0.6908077001571655, 0.2653011679649353, -32682974], [0, 0, 0, 1]],
          "opacity": 1.0
        },
        {
          "name": "PLI Transmittance",
          "source": "precomputed://https://zam10143.zam.kfa-juelich.de/chumni/nifti/cb905d54437734b39807e252ef8aa68bc6ac889047fbebbafd885490/BI-TIM",
          "shader": "void main(){ float x = toNormalized(getDataValue()); if (x > 0.9) { emitTransparent(); } else { emitRGB(vec3(x * 1., x * 0.8, x * 0.8 )); } }",
          "transform": [[0.7400000095367432, 0, 0, 11020745], [0, 0.2653011679649353, -0.6908077001571655, 2533286.5], [0, 0.6908077001571655, 0.2653011679649353, -32682974], [0, 0, 0, 1]],
          "opacity": 1.0
        },
        {
          "name": "T2w MRI",
          "source": "precomputed://https://zam10143.zam.kfa-juelich.de/chumni/nifti/cb905d54437734b39807e252ef8aa68bc6ac889047fbebbafd885490/BI-MRI",
          "shader": "void main(){ float x = toNormalized(getDataValue()); if (x < 0.1) { emitTransparent(); } else { emitRGB(vec3(0.8 * x, 0.8 * x, x * 1. )); } }",
          "transform": [[0.7400000095367432, 0, 0, 11020745], [0, 0.2653011679649353, -0.6908077001571655, 2533286.5], [0, 0.6908077001571655, 0.2653011679649353, -32682974], [0, 0, 0, 1]],
          "opacity": 1.0
        },
        {
          "name": "MRI Labels",
          "source": "precomputed://https://zam10143.zam.kfa-juelich.de/chumni/nifti/cb905d54437734b39807e252ef8aa68bc6ac889047fbebbafd885490/BI-MRS",
          "transform": [[0.7400000095367432, 0, 0, 11020745], [0, 0.2653011679649353, -0.6908077001571655, 2533286.5], [0, 0.6908077001571655, 0.2653011679649353, -32682974], [0, 0, 0, 1]],
          "opacity": 1.0
        }
      ]
    }
  },
  "referenceSpaces": [
    {
      "name": "Big Brain (Histology)",
      "fullId": "minds/core/referencespace/v1.0.0/a1655b99-82f1-420f-a3c2-fe80fd4c8588"
    }
  ]
}

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1. Currently, kg-dataset-previewer is used to resolve the preview URL. This is very likely going to change in the future. ↩