==Peddi Sai Varshith: 2021 Google Summer of Code caMicroscope-Hardware Integration==

Video Presented on 19 August 2021

[[Video(https://www.youtube.com/watch?v=iXwYq9Hzv1k)]]


='''Google Summer of Code Challenge'''=
Title: Integrate an optical microscope with a camera and motorized stage - Collaboration with FDA

Mentors: Nan Li and Brandon Gallas

Overview: The FDA has created eeDAP, an evaluation environment for digital and analog pathology. eeDAP is a software and hardware platform for designing and executing digital and analog pathology studies where evaluation regions of interest (ROIs) in the digital image are registered to the real-time view on the microscope. This registration allows for the reduction or elimination of a large source of variability in comparing these modalities in the hands of the pathologist: the field of view (the tissue) being evaluated. There are many other research and commercial use cases for eeDAP. eeDAP is written in Matlab, which is commercial software that requires a license and is not designed for digital pathology image viewing and annotation. We would like to move the eeDAP features into caMicroscope. The user will be able to control a digital camera and an x-y programmable microscope stage, with caMicroscope. It may or may not be useful to consider use of custom tile sources in openseadragon.

='''About Peddi Sai Varshith and the 3D Printed Hardware'''=
Peddi Sai Varshith, is a 3rd-year undergraduate student at Keshav Memorial Institute of Technology, Hyderabad, India. His skills include proficiency in python (along with NumPy, Pandas, Matplotlib), JavaScript, Git, GitHub, and web development. He is a part of a technical club (Recurse) at college, which organized Tech-fests to encourage the students to have the taste of STEM competition.

The hardware system in this video consists of a motorized x-y-z stage which we designed and fabricated in-house with our 3D printer. This is fitted with an optical objective lens of magnification 40x and an eyepiece of 10x, a bright field light source and a digital camera to take WSI images of biopsy sample slides. We have developed a GUI which controls the x-y-z motion of the motorized stage, to perform step and repeat process to get an array of images. These images are then cropped, stitched and converted into a set of image tiles in a folder. The WSI image thus formed is further processed using a filtering algorithm to deliver five sets of WSI images with decreasing resolution and increasing field of view, thus completing the image pyramid data.