The second point is quite simple: in overwhelming number of imaginable scenarios there is no need for simultaneous display of 2D and 3D panels. So, 3D view should be resizable to the whole screen (by “double clicking” or something like that), and rendering three 2D images and 3D image at the same time would not be necessary. In other words, four panels view should be easily replaceable by one panel view (see Fig. 5 below). It will save about a half of the network bandwidth, let alone – CPU and GPU resources, and will make it possible to render 3D with adequate resolution at reasonable speed.
Fig. 5, a and b: Resizable and “zoomable” 3D view panel. 3D viewer shows arbitrarily positioned 2D sectioning plane.
4. The “Qute Brain Browser” features:
- Simple, self-explanatory interface, which includes file browser, so it opens the image after single click on the file name.
- Resizable 2D and 3D image panes.
- Combination of mesh-rendering and voxel based rendering in 3D
- 3D slicer: one plane that cuts the 3D view in any position at arbitrary angle.
- Combines mesh-based rendering with texture-based rendering. Mesh is build in real time (only if necessary) using volume-to-mesh utility from OpenVDB library.
This is an example of 3D view which combines mesh-based and pixel-based rendering.
Fig. 6: Mesh rendering vs. oxel-based rendering .
Below we demonstrate some example of 3D view rendering images at different resolutions:
Fig. 7: 100 microns resolution
Fig. 8: 40-microns resolution
Fig. 9: 1-micron resolution, before segmentation
Fig. 10: 1-micron resolution after image segmentation
As I said already, due to high density of cellular elements and monotonous colors revealed by Merker staining procedure, it is difficult to select an adequate parameters of camera, lighting conditions, material colors etc. to render a representative volume of human cortical area in 3D at 1 micron-resolution level. So, the picture above does not look informative enough yet. To the best of my knowledge, this is the first 1-micron resolution reconstruction, based upon processing of 80 registered serial sections of human brain. Again, this is “work in progress”, so this result might improve in a nearest future.
4. Additional features of the “Qute Brain Browser”:
Supports different file formats:
- BIG TIFF
- BMP, JPG, JPEG, PNG… and more.
- OpenVDB – the last, but not the least. (The advantages of OpenVDB format in a context of dynamic sparsity of microscopy datasets will be discussed later.)
Additionally, the “Qute Brain Browser” also can be used to read atlases and templates (for example, ICBM template and ICBM labels)
Fig. 12. ICBM template and labels images.
Several labels can be selected simultaneously to be used as a “mask” for selective visualization of specific cortical and sub-cortical structures in 3D, as it shown below:
4. Instead of a conclusion: the bumpy road to multi-modal human brain atlas.
To conclude, I think the examples presented above, if nothing else, prove that the importance of 3D rendering of high resolution brain images is significantly underestimated and underdeveloped in current implementation of HBP’s “BigBrain Viewer” (as well as in the “Atelier-3D”). As a result, its presently available features and functionality are grossly inadequate. However, the “HBP Human Brain Atlas”, according to the description of HBP Subprojects , supposed to be “the greatest goal” of the sub-project two (SP2) of HBP: “One of the greatest goals of SP2 is to develop the HBP Human Brain Atlas, which can be used by neuroscientists all over the world, in neurosurgery and as a basis to understand the differences between the healthy and diseased brain.” It will be very unfortunate if such limited functionality will be used as a prototype for the graphic interface in so well advertised and, supposedly, even better founded Human Brain Atlas development project.