Histological Whole Slide Imaging

Whole Slide Imaging denotes the technique of digitalizing a whole histological slide for computer based analysis in contrast to the examination of a small section of a slide under a microscope. This technique is widely used in research since it allows a complete quantification of given parameters (such as proliferating cells, fat distribution or the course of vessels) throughout the entire tissue sample.

  • Within the context of the Virtual Liver Network the aim of using Whole Slide Imaging on a serial section is the 3D-reconstruction of the whole organ - in our case the whole liver of mice or rats – instead if merely examining individual sections of the organ.
  • The preparation of whole slide sections starts with the explanted liver being fixed in formalin and embedded in a block of paraffin (on the image it is shown on the left). Hereby the orientation of the whole organ is important to facilitate the subsequent detection/ registration of the course of the vessels. The whole block is then sliced into 4 µm thick serial sections, resulting in 500 – 2500 consecutively numbered sections. To cut the block, a rotation microtome with single-use blades is used (on the image it is shown in the middle). A slide transfer system aids in transferring the sections away from the blade into a cold water basin with the help of flowing water. The sections are then transferred into a warm water bath to straighten them and placed on a slide afterward (on the image it is shown on the right).
  • A crucial part of the process is to cut the organ with as few interruptions as possible to avoid disposal of faulty sections so that each section is of high quality and can be used for registration later on. Fur, suture material, calcifications, tissue consistency, fissures or unfavorable temperatures may affect the section quality negatively.
  • Another challenge of working with histological samples is that the liver lobes differ in size and their position in the block might be affected by fissures or during the process of embedding itself.
  • Depending on the aim of the block the tissue is stained with specific stainings to expose certain tissue parameters (e.g. proliferation). To be able to analyze several parameters different stainings can be applied alternatingly. The sections are then digitalized using a whole slide scanner, resulting in a total data volume of 1 – 2 Terabytes. The individual slides can be analyzed separately. In our case they are arranged on top of each other to reconstruct and visualize the organ in its entirety.
  • Authors: Uta Dahmen, Stephanie Lange, Michael Schwier

  • Image: Uta Dahmen, Stephanie Lange, Michael Schwier, Iryna Ilkavets

  • Comprehensibility: 
    Average: 5 (1 vote)
    (1=bad 5=excellent)