The purpose of this post is to outline a little bit about the background to QuPath, describe where it is now, and give some personal reflections on where it’s going.ĭisclaimer: All words and opinions are my own - and not those of any past or future employers. However, after an initial flurry of updating activity, QuPath has not changed much since its first public incarnation.
CELLPROFILER NOT RESPONDING SOFTWARE
Since then the software has been downloaded thousands of times, referenced in various academic publications, taught in courses throughout Europe, and is being used in labs across the world. QuPath was released open source at the end of 2016. This lets you focus on the most interesting parts of your work… and also the parts that lend themselves to being published in academic journals What is this blog all about? handling large images, interactivity, visualization).
QuPath doesn’t try to do everything, but for the things that it does do it tries to give lots of helpful features and shortcuts to make otherwise difficult tasks as painless as possible.Īnd because it’s open source, extensible and scriptable, if you’re computationally-minded and looking to develop new image analysis algorithms, then QuPath can give you a platform that takes care of a lot of the the essential-but-mundane tasks for you (e.g. You might also want to try QuPath for other applications. ImageJ, Fiji, CellProfiler, icy & ilastik) is its support for whole slide image analysis and digital pathology.īroadly, if you find yourself working with ultra-large 2D brightfield or fluorescence images (perhaps 40 GB in size), potentially containing millions of cells that you want to be able to identify and classify, you might well want to try QuPath. One of the things that distinguishes QuPath from other open bioimage analysis tools (e.g. If you’re reading this, there’s a good chance you’ve already encountered it. QuPath is open source bioimage analysis software, available at.
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