3D reconstruction of serial whole slide sections

In order to understand liver functions, the physiology and morphology of microscopic tissue sections are invaluable. However, one section is extremely thin (4 µm) and thus captures only a small fraction of the whole organ. This means disregarding a lot of tissue information as well as their 3D correlation.

  • Scientists in the Virtual Liver develop methods to digitally reconstruct the organ in 3D based on serial tissue sections. The main challenges for this are deformations of the tissue which are introduced during the cutting process and the placement of the section on the slide. Thus consecutive slides cannot simply be stacked on top of each other to regain the 3D object.
  • Therefore a so-called registration algorithm was developed. This algorithm analyzes two consecutive sections for corresponding structures - e.g. vessels that are expected to continue smoothly through the organ. Based on this analysis the digital image is deformed, so that those corresponding structures match again.
  • The video shows three different stages of this process: the left side shows a run through a stack of consecutive serial tissue sections in their initial stage – directly from the slide scanner. As we can see the position from one slide to the next in general does not match at all. This middle shows the result of the first registration step which compensates coarse deformations. The right side shows the result after a refinement step, which is aimed at compensating misalignments in more detail.
  • Further reading: Registration of histological whole slide images guided by vessel structures
  • Author: Michael Schwier

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