- YouTube playlists with tips, tricks & explanations
- Experimental art with modified drawing tools
- Creating annotations for the central region, inner margin and outer margin
- Part 2: A proposed change to help with using multiple classifications in QuPath
- Part 1: A way to approach multiplexed images with QuPath
- Improved image support (again) - including for 32-bit multichannel Vectra images
- Tips for setting cutoff thresholds to determine positive cells to match visual estimates
- Lots of QuPath updates & improvements! Read how to try them out now.
- Print the methods & fields associated with an object, as a quick help when writing scripts.
- For every image in a project, count the total number of objects, the total number of annotations, & the number of annotations split by classification - quickly.
- Export annotations as labelled images, using tiling if needed.
- Different ways to trace contours... and what they mean. Important for writing new QuPath algorithms (e.g. for cell detection), or exchanging regions between software.
- Export annotated regions as binary masks. Also, create new annotations from binary masks.
- Create a fixed-size rectangle annotation, for analysis or export.
Do real, customizable image processing with QuPath & ImageJ.
Grab regions, apply color deconvolution, detect & measure stained pixels, send results back.
Enter the world of ImageJ, grabbing pixels as ImagePlus objects for further processing.
Also: an introduction to QuPath data structures & methods for accessing pixels generally.
- Identify and address out-of-memory troubles when analyzing large images.
- Merge together the results from the previous script, to get one mega results table.
- Export all the measurements for all the annotations in a project, in an orderly way.
Discover QuPath through scripting. Or discover scripting through QuPath.
Either way: a series on QuPath & scripting.
- An overdue update on QuPath: What it is, where it's from & where it's going.
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