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Citation reference (copy and paste into your CV): 

"Image data analysis from microscopy and MRI using QuPath - P2P Teaching, Season 3". (November 10th, 2022). 2 hours workshop, Bioinformatics Support Hub, Cushing/Whitney Medical Library, Yale School of Medicine.  https://guides.library.yale.edu/imaging_p2p 

Workshop Summary:

This workshop was part of the third season of the Peer-to-Peer Teaching sessions. These are taught by our own community members to fill knowledge gaps and keep up with the accelerated pace at which bioinformatics grows. This season we are pleased to announce sessions covering * Image analysis methodologies (imageJ and QuPath) * Omics analysis in R and/or Python * Biomedical Data analysis using the clusters * Statistical analysis software (Prism) *Science communication (Illustrator).

This session on "Image data analysis from microscopy and MRI using QuPath" was designed and delivered by Zachary Gursky, PhD, from the department of Anesthesiology, Section of Perioperative Adult Anesthesia.

Summary:

     In modern biology research, tremendous amounts of data are generated using diverse imaging methods such as fluorescence microscopy and magnetic resonance imaging. To generate quantitative data from these images (e.g., counting cell number, quantifying fluorescence intensity, determining the area fraction of tissue expressing a marker), many different analysis softwares have been created. The software "QuPath" (abbreviation of "Quantitative Pathology & Bioimage Analysis") is free, open-source, does not require coding experience, and can analyze many different image file types. Thus, QuPath is a versatile program that can be used in many different kinds of biological experiments, as is proof by its 2000+ citations since its development in 2017.

     In this session we analyzed microscopy and MRI example images. You were allowed to  interact with the software, open and analyze image data and you learned where to access further tutorials and online assistance for more advanced features. In addition to hands-on learning, you also learned how to troubleshoot an image of your own with QuPath, and briefly discussed alternative software for image analysis to supplement QuPath's functions.

This workshop is designed for: 

•  biomedical researchers with an interest in quantitative image analysis of fluorescence microscopy images or structural MRI images. No coding experience is necessary. 

You have learned how to: 

1. Open and organize images into a QuPath project.
2. Automate cell number quantification and phenotyping of those cells in a fluorescence microscopy image.
3. Use a machine-learning classifier to quantify the area fraction of different tissue types in an MRI image.
4. Apply analyses to multiple images for reproducible science.
5. Locate tutorials and online resources for advanced applications of QuPath beyond the functions covered in this workshop.

Duration: 2 hrs

Instructor: Zachary Gursky, PhD