Visualization of 3D cell data


I am looking for advice on how to get started with the following problem: I have 3D numpy arrays that are for example 100x300x300 and represent a volume that holds cell data. It is therefore not a point cloud or mesh but a medical 3D image with voxel values. Additionally, I have bounding box data with Position Z,Y,X and Length Z,Y,X. Previously, I have visualized this with napari. However, it is lacking 3D capabilities. I am therefore looking into more sophisticated visualization techniques but am not sure how to use this data with ParaView. I would welcome any pointers or other suggestions.

Thank you and kind regards!

Just open our data with ParaView.

Thank you for your suggestion. I have tried loading a numpy array as .npy file and a .h5 file with all the arrays without success. While loading a csv file with bounding box centroid and lengths works, I don’t know how to turn that raw data into a visualization.

See here for some info:

Also: How to open ".npy" file or convert ".npy" file to Paraview format?

Sorry, I have tried turning the numpy volume into a .vtr file and .mhd file to render the volume in paraview. However, regardless of the representation I choose in paraView, I either only see an outline of the volume or a solid volume. Do you know what I am doing wrong?

Switch representation to surface ?

I have tried Surface but then it just becomes a solid colored volume so I still cannot see the content. Even with opacity, there is nothing in the volume. If I visualize the same file with napari or pyvista, I can see the content inside the volume.

You are looking for VolumRendering or Slice.