QuPath Workshop April 2018

Updated 2,208 Days AgoPublic

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This document aims to compile the documents that were created during the QuPath Workshop and Hackathon which took place from April 17th till April 20th

Questions & Answers

Is it possible to open confocal images (lsm files)?

Yes. But you'll need the QuPath BioFormats Extension, which you'll need to install according to the instructions on GitHub

Can there be more than 2 stains?

are z-stacks supported?
are bit depths other than 8-bit supported?
can a custom version of ImageJ (e.g. FIJI) be used instead of the one shipped with QuPath
can the macro runner run imageJ macros (.ijm) only or also scripts written in a different language?
Can we set a different threshold of cell detection in a specific area ?
cell detection behaviour on fluorescence images
Would it be possible to duplicate an annotation from one z plane to another z plane in the same image?
How many channels are supported by QuPAth for the confocal image? I have 4 channels, I can modify brightness/contrast for all of them however cell detection and measurements are possible only with 3 channels and not with 4th one.
Does changing brightness/contrast affect measured values?
Is there a batch mode?
can we measure inside the overlay that was sent from imageJ?
Can we do pixel classification?
What other objects besides cells can be classified?
Can there be different staining definitions for the cell detection?
Set Image Type as “Other” -> Can define Stain Vectors by annotation
Can we have more than 2 stains?
Can we make an annotation out of a classification result?
How do I set the resolution of an image manually?
is there a way to make “close project” also close the currently open image?
Is it possible to add measurements to regions from ImageJ? See this Blog Post
How do we detect other things like fibers or differently shaped cells?