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GSoC2021_caMicroscope_Peddi_sai_varshith.md

GSOC 2021 Final Work Product


What's So Special About this Project?

eeDAP is an evaluation environment for Digital and Analog Pathology. The software has two modes one for digital WSI image evaluation and other for real time comparison of analog image and digital WSI image. The key features or process of the eeDAP have to be developed such as the registration of the digital and analog images. The registration is done by the study administrator to get the relation between WSI image coordinates and x-y stage coordinates

Link: eeDAP


Aim

The aim is to incorporate the methodology of eeDAP and hardware system into the camicroscope as a web service plugin to add additional functionality. The eeDAP has global registration which involves three local registrations. The local registrations are done by taking unique regions of interest on the microscope and selecting the similar regions on the digital WSI image. Both the images are then compared, and the corresponding coordinates are registered locally. Similarly, the process is repeated for two more times. One ROI coordinate is taken as reference and the global registration/transformation bias is calculated. This transformation bias can be used to relocate the x-y stage when new coordinates of the WSI image are given.

Project Summary

  • Feature: MicroRT-Mode
  • Added Features:
    • Provide a way to do realtime comparative analysis of the digital WSI with microscope image.
    • Incorporated the methodology of local registration and global registration of eeDAP in the camicroscope.
    • Added a Live stream viewer of microscope on client machine.
    • Developed an automation movement of lens on microscope after calculating the transformation values.
    • Developed an interface to client to interact with microscope.
    • Provided a valid authentication in the registration Process.
    • Log previous x, y stage positions to calculate the relative steps which are required to move the x-y stage.
    • Created Different api's for each functionality.
  • Pull Requests:

Project MileStone(Features Developed)

  • First MileStone
    • Uploading a WSI Image.
    • Created a Interface for Previewing WSI image.
    • Developed crop option which enables the user to crop the region on WSI at any scale.
    • Provided a service to live stream the microscope view to client on same network.
  • Second MileStone
    • Added authentication to user for performing registration.
    • Developed template-matching algorithm for detecting common region from both the images(WSI,slide).
    • Created an api for calling registration.
    • Designed the buttons to control the microscope.
  • Third MileStone
    • Developed a hardware code for interacting with raspberry PI and hardware modules.
    • Developed different api's on server for performing different functionality on client actions.
    • Developed a log file for storing the coordinates and storing the wsi and stage image information.
    • Performing transformation of selected WSI coordinates.
    • Developing a automation movement of lens on microscope.
    • Auto Focusing the image based on laplacian value.
    • Developed a final interface which contains preview of both WSI image and slide view.

Video Guides:

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