There is no 3D model displayed after converting the nrrd format or tif images into the required data for neuroplanner

[scorpio921]

code

  import numpy as np
  from cloudvolume import CloudVolume
  from cloudvolume.lib import Bbox
  import nrrd

  print(dir(nrrd))

  nrrd_file_path = './I.nrrd'
  data, header = nrrd.read(nrrd_file_path)

  print("Original NRRD data shape:", data.shape)
  print("Original NRRD data type:", data.dtype)
  print("Data min:", np.min(data))
  print("Data max:", np.max(data))

  normalized_data = ((data - np.min(data)) / (np.max(data) - np.min(data)) * 255).astype(np.uint8)

  print("Normalized data min:", np.min(normalized_data))
  print("Normalized data max:", np.max(normalized_data))
  print("Normalized data type:", normalized_data.dtype)

  output_path = 'file:///path/to/nrrd'
  volume = CloudVolume(output_path, info={
      'type': 'image',
      'data_type': 'uint8', 
      'num_channels': 1,     
      'scales': [{
          'resolution': [2,2, 2],  
          'size': normalized_data.shape,  
          "key": "d2",  
          'chunk_sizes': [[64, 64, 64]],  
          'encoding': 'raw'  
      }]
  }, compress=False)

  volume.commit_info()

  bbox = Bbox((0, 0, 0), normalized_data.shape)

  volume[bbox] = normalized_data

  downloaded_data = volume[bbox]
  print("Downloaded data shape:", downloaded_data.shape)
  print("Downloaded data type:", downloaded_data.dtype)
  print("Downloaded data min:", np.min(downloaded_data))
  print("Downloaded data max:", np.max(downloaded_data))

  print("TIFF data has been converted and uploaded to precomputed format.")

[jbms]

By 3-d model, do you mean volume rendering in the 3d panel?

You have to enable that by selecting "Volume rendering" in the "Rendering" tab of the layer.

[scorpio921]

@jbms Thanks ，you are right, but, I have one more question. Why doesn't my 2D image have rendering nodes and the 3D model looks very blurry? Do you know why