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  • Dhruti Pattabhi

Using Software for Research: Digital Pathology through QuPath

Updated: Jan 29

You’ve powered through your experimentation and now the time has come to analyze your data. The slides come in from the histology lab and all of a sudden you’re staring straight into a microscope– face to face with a mass clump of cells. Here’s where your dilemma starts. Do you spend your remaining summer hand counting each of the positive cells or use a computerized counting mechanism to analyze them bias-free?


If accuracy is indeed what you’re looking for, the latter option arguably sounds more attractive. Quantitative Pathology– or QuPath– is a software specifically meant for analyzing digital pathology. With a wide range of image applications and user-friendly system, it is suitable for histology and pathology research worldwide— here’s an overview of QuPath.



Screenshot of QuPath

Caption: Analysis of tissue. Retrieved from the official QuPath site.


QuPath supports a variety of domains including macOS and Windows. Installation and troubleshooting information is directly available on the website.


Once you’ve opened the software, QuPath estimates the image type based on the staining dye used. However, it’s probably best to manually set or verify the image type. Once the image has been opened, a prompt requests you to confirm the image type. Upon completion, using the “Annotations” tab, you can set a region for the software to analyze. The regions can either be selected manually or by gradually applying color/density thresholds to the image. These areas will be recognized as “objects” to QuPath— things the software can detect, identify, and classify.


For further inspection of these regions, the software is equipped with various evaluation tools. Using the “Analysis” tab, you can run a “cell detection” or even a “positive cell detection”. These options filter cells or other objects within your annotations. To implement either of these options, a list of parameters pops up. While you could always use the default parameters, chances are that you know your research well and probably choose to tweak the parameters of your images yourself. Some of these parameters include maximum and minimum areas, thresholds, radii, and background intensity. These are useful in ensuring precise image analysis. Once you are satisfied with the implementations, the “Run” button will display a visual depiction and a count of the detected objects. Both positive and negative objects will be counted separately, so it is possible to filter either or.


Of course, there are many other ways to utilize QuPath in your pathological/histological research. For further information and specifics, be sure to use the resources and tutorials below!



Application of Qupath:



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