Annotating pathology specimens for class activities

July 25, 2019

Developing an understanding of disease processes requires consideration of both the macroscopic and microscopic appearances of diseased tissue. At the University of Queensland, Dr Suja Pillai and her colleagues have utilised annotations to mark-up images of virtual slides as well as gross pathology specimens to share with students in the first two years of the Graduate level Medicine program.

The University of Queensland Integrated Pathology Learning Centre houses potted specimens and virtual slide collections, both of which are used within tutorial sessions. To complement face-to-face sessions and allow students to preview or review the tutorial, online materials have been developed for each topic covered. The online materials focus on correlating macroscopic and microscopic features of diseased tissue, comparing these to normal specimens. Annotated layers on virtual slides and macroscopic images make up a portion of this material.

Example annotation layer focusing on the microscopic features of Paget's Disease.

Using Slice, a team of academics have worked together to create a collection of layers that annotate key features on hundreds of images. One or two layers are created for each image. The first locates features and asks students to identify the structure highlighted, or its function. Students can then discuss with their tutor in class. In some cases, a second layer reveals the answers and is provided to students after the tutorial. Students access the layers by following hyperlinked images in lectures and tutorial material, as well as within Smart Sparrow lessons.

Dr Pillai has found the Slice annotation tool essential to this practice.

"Increasing class sizes in medical schools has made the use of light microscopy unrealistic. Slice has enhanced the learning environment by enabling different magnifications and dissecting through the whole of abnormal tissue morphology compared with static digital images/microscope that can only depict a selective area of the original pathology and fail to explain the whole disease process. Furthermore students are able to access it at any time, place or on any device leading to more meaningful communications among students."

The BEST Network recently released public layers functionality (to learn more visit the BEST Knowledge Base). Dr Pillai and her team have generously made some of their post-tutorial annotation layers public to demonstrate the resources created for their students:

  1. Squamous Cell Carcinoma
  2. Atherosclerosis
  3. Paget's disease of bone
  4. Granulomatous Inflammation (Tuberculosis)
  5. Atrial septal defect
  6. Intussusception of intestine
Example pre-tutorial annotation layer demonstrating intussusception. Students are asked to identify structures. See the post tutorial layer here.

The team would like to acknowledge the contributions of Dr Mohit Shahi, Dr Archana Sudarsan, Dr Glenda Gobe and Dr Nicholas Hawkins in the creation of annotated layers for this work.

Use the new public layers filter to view other shared annotation layers here.

To help us build a database of knowledge around our Slice images, academic members are invited to share their annotation layers with the community. To make an annotation layer public see our instructions here. If you have any questions about Slice or public annotation layers please email me at