<aside> 💡 With the advent of technology, medical sciences have also seen an advancement and improvement from the traditional approaches used in various fields. Histopathology is yet another field which has been, and can be further benefitted from the technology. Traditionally, after the slide development the pathologists were required to look at each of the slides individually in order to diagnose. But now, using Volume Rendering techniques, one could generate a 3 dimensional model of the tissue using the slides enabling better histopathologic analysis.

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Layout

Screenshot of Project's feature

Goal 🚀

We aim to create an application which provides a user with the following functionalities:

1. Send a set of virtual slides (.svs, .tif, etc.)
2. Generate a 3D volume using the provided set of slides
   1. Given that the slides can be very large in size, come up with a suitable architecture to manage data.
3. Provide a set of UI based functionalities:
   1. Add a Slicing feature using an arbitrary plane or axis-aligned planes
      1. View the Cross-Section
   2. Select a sub-volume
      1. Viewing certain artifacts based on their color. Refer to this for further information.
      2. Draw a ROI
   3. Zoom/Scaling the volume with replacement of the current resolution image with an appropriate higher resolution section.
   4. Annotations in 3D → provide an option to annotate artifacts in 3D
      1. Some WSI's provide polylines → Generate a marked region in 3D rendering from a set of points.
4. Alignment of different slides
   1. When we stack multiple slides, it is important to understand which section of each slide corresponds to a section in another.
   2. Furthermore, two slides created from the same tissue may not be aligned from corner to corner so it is important to correct such misalignments

Source Code

agam-kashyap/3Dhistopathology

Installation Guide on Ubuntu

Inviwo Setup

1. Refer to the inviwo documentation.

<aside> 💡 Ensure the ubuntu version supports Qt

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1. Use the Cmake GUI to select the necessary modules and add CMAKE_PREFIX_PATH