3d rendering of nii volumes

[PolarBean]

by setting the alpha channel to be the same value as the channel (multiplied by some large value) it is possible to render great semi transparent views of precomputed volumes in the volumetric rendering window.
ie; https://tinyurl.com/bfay8aem
and: https://t.co/pi2k3D3Wit

here is an example of a shader with the magma colormap (this is applied in the first link)

// iav-colormap-is-magma

      vec3 magma(float t) {
      
          const vec3 c0 = vec3(-0.002136485053939582, -0.000749655052795221, -0.005386127855323933);
          const vec3 c1 = vec3(0.2516605407371642, 0.6775232436837668, 2.494026599312351);
          const vec3 c2 = vec3(8.353717279216625, -3.577719514958484, 0.3144679030132573);
          const vec3 c3 = vec3(-27.66873308576866, 14.26473078096533, -13.64921318813922);
          const vec3 c4 = vec3(52.17613981234068, -27.94360607168351, 12.94416944238394);
          const vec3 c5 = vec3(-50.76852536473588, 29.04658282127291, 4.23415299384598);
          const vec3 c6 = vec3(18.65570506591883, -11.48977351997711, -5.601961508734096);
      
          return c0+t*(c1+t*(c2+t*(c3+t*(c4+t*(c5+t*c6)))));
      
      }
    
void main() {
  float raw_x = toNormalized(getDataValue());
  float x = (raw_x - 0.0000000001) / (0.23) - 0.0000000000;

  
    vec3 rgb;
    rgb=magma(x);
    emitRGBA(vec4(rgb*exp(0.0000000000),
                  clamp(x*255.0,0.0,256.0)));
  
}

alpha can either be a single digit or an array of values with the same shape as a single channel of the data.

The issue with this is that in many cases it can screw up the XY 2d views since the same shader is applied to both volumetric rendering and the 2d view. So some trickery may be required (for instance loading them as seperate but linked layers).

Another requirement is making sure the volumetric rendering option is specified here:

And I am not sure if this is available in your current branch of neuroglancer.

All the best,

Harry