Posts
-
Update on this blog
Blog not maintained, but QuPath is! -
QuPath v0.2.0-m8 available
Eighth milestone on the path to QuPath v0.2.0 -
QuPath v0.2.0-m6 available
Sixth milestone on the path to QuPath v0.2.0 -
Changing the hierarchy
What is different in v0.2.0-m6 - and why it matters -
QuPath news
Funding (finally!), current developments & future plans -
QuPath v0.2.0-m5 available
Fifth milestone on the path to QuPath v0.2.0 -
Building QuPath
How to build QuPath from source & run from eclipse -
Scripting in v0.2.0-m4
What's changing and why - an update -
QuPath v0.2.0-m4 now available
Fourth milestone on the path to QuPath v0.2.0 -
QuPath v0.2.0-m3 now available
Third milestone on the path to QuPath v0.2.0 -
Come work with me on QuPath! (07/19)
New Research Fellow position at the University of Edinburgh (Updated July 2019!) -
A new place to get help
QuPath discussion forum moves to image.sc -
A new milestone
First (and second) milestone releases of QuPath v0.2.0! -
QuPath video tutorials
YouTube playlists with tips, tricks & explanations -
Drawing tools & the object hierarchy
Experimental art with modified drawing tools -
Creating annotations around the tumor
Creating annotations for the central region, inner margin and outer margin -
Supporting multiple classifications: a proposed change
Part 2: A proposed change to help with using multiple classifications in QuPath -
Multichannel fluorescence & multiple classifications
Part 1: A way to approach multiplexed images with QuPath -
QuPath + Bio-Formats update
Improved image support (again) - including for 32-bit multichannel Vectra images -
Detecting positive cells
Tips for setting cutoff thresholds to determine positive cells to match visual estimates -
QuPath updates!
Lots of QuPath updates & improvements! Read how to try them out now. -
Script of the Day: Finding methods
Print the methods & fields associated with an object, as a quick help when writing scripts. -
Script of the Day: Count annotations in a project
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. -
Script of the Day: Exporting labelled images
Export annotations as labelled images, using tiling if needed. -
Notes on contours
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. -
Script(s) of the Day: Exporting & importing binary masks
Export annotated regions as binary masks. Also, create new annotations from binary masks. -
Script of the Day: Create new annotations
Create a fixed-size rectangle annotation, for analysis or export. -
Script of the Day: Whole slide image processing with ImageJ
Do real, customizable image processing with QuPath & ImageJ.
Grab regions, apply color deconvolution, detect & measure stained pixels, send results back. -
Script of the Day: Extracting image regions to ImageJ
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. -
Script of the Day: Memory monitor
Identify and address out-of-memory troubles when analyzing large images. -
Script of the Day: Merging annotation results
Merge together the results from the previous script, to get one mega results table. -
Script of the Day: Batch exporting annotation measurements
Export all the measurements for all the annotations in a project, in an orderly way. -
Introducing 'Script of the... Day?'
Discover QuPath through scripting. Or discover scripting through QuPath.
Either way: a series on QuPath & scripting. -
QuPath: Past, Present & Future
An overdue update on QuPath: What it is, where it's from & where it's going.
subscribe via RSS