Image.sc forum posts
(and some GitHub)
A quick reference list - idea for expanding to a full page from Mark Zaidi
Alignment related posts and workflows
**Requires more than just QuPath, but allows deformable registration!!
> Registration of whole slide images at cellular resolution with Fiji and QuPath
QuPath:
> Image alignment (affine) and object transfer across N images
> QuASI: GitHub - MarkZaidi/QuASI: List of QuPath scripts for alignment and stain deconvolution of whole-slide images
> ABBA [experimental] - A Fiji + QuPath workflow for Mouse Brain Slice registration to the Allen Brain Atlas
> @phaub image-combiner-register-images-and-create-project-entry/50484
CluPath: Speed up certain QuPath functions using your video card, from Robert Haase, @haesleinhuepf.
CellPose plugin - requires Python installation, CUDA, etc., but the end result is cell segmentation with the potential for useful cytoplasmic outlines.
Visualization of complex classifications
CytoMAP related - High plex analysis
QuPath to CytoMAP and back - perform unsupervised clustering of your QuPath cells or objects. Alternatively generate tSNE plots and create gates for use in QuPath.
Neighborhood analysis of QuPath segmentation results using CytoMAP
@phaub series
Complex scripts and plugins from Peter Haub, @phaub
qupath-scripting-1-using-clupath-to-save-smoothed-image-regions/49525
qupath-scripting-2-using-clupath-and-ij-to-show-image-with-additional-local-threshold-channel/49962
qupath-scripting-3-apply-colorlut-or-invertedlut-to-channel/50368
qupath-scripting-4-image-combiner-register-images-and-create-project-entry/50484
qupath-scripting-5-export-image-and-rois-to-imagej/50636
qupath-scripting-6-customized-3-stain-color-deconvolution/50864
qupath-scripting-7-clij-multi-gpu-processing/52129
Mixed topics
Sara McArdle @smcardle
>RareCellFetcher- a tool for annotating rare cells in QuPath
>Method for transferring Results from ImageJ back into QuPath objects
Mark Zaidi @Mark_Zaidi
>Universal StarDist for QuPath - Transfer Pretrained Models Across Modalities With Ease
QuMark: GitHub - MarkZaidi QuMark: A standardized benchmark for evaluating QuPath performance
Andreas Poehlmann @poehlmann
> Paquo - read/write QuPath projects from Python
@research_associate
> Not much scripting, but an overall guide to QuPath functionality
>Tumor invasion zones, stroma by distance - creating zones by distance
Now tested, it works very well, and only took a few minutes to set up!: Jeff Hass @JeffHaas
> QuPath script: Telegram Messenger Alerts - How To Set Up
Pretty great colocalization reference post from Jan Brocher, @biovoxxel
> Colocalization analysis advice, large collection of links