QuPath

Open source software for bioimage analysis.
No longer active here - ask about me at

[QuPath @QuPath]

Find out about the latest QuPath developments as part of the @GloBIAS_ series 'Current and future plans for essential BIA tools' *today* (26 March, 4-5pm CET)

Details & registration at https://t.co/9Lhwa3em1s

[LJI Microscopy Core @LJIMicroCore]

📢Announcing a QuPath Workshop 📢 February 24-25, 2025, in San Diego, CA, at the La Jolla Institute for Immunology. This year’s event will be all about Multiplex Immunofluorescence Analysis. The workshop will be followed by an 🎉 Advanced QuPath User’s Meeting 🎉- Feb 26

[QuPath @QuPath]

Join us at the Virtual I2K meeting next week!
Lots of image analysis tutorials - including 3 about QuPath & 1 about InstanSeg 😀💻🔬

[BioImaging North America @BioimagingNA]

Virtual I2K starts next Monday, Oct 28!!!🎉

34 exciting tutorials on #OpenSource #ImageAnalysis

Register (for free) today!!
https://t.co/I0cqzyC0FH

Can't make it? Watch on YouTube after the event:
https://t.co/WYBME3rQgJ
2022 & 2023 tutorials available now!

[Luke Gamon @lgamon]

Love this this just… works? Installed on my M3 MBP and was segmenting images in a matter of minutes 👏

[Pete Bankhead @petebankhead]

But what if you don’t know or like @QuPath?

Firstly, I’m outraged.

Secondly, we want you to use the software that's best for you - so we've made sure you can run InstanSeg on smaller images with @deepImageJ

https://t.co/YVdmGSycXy

[Pete Bankhead @petebankhead]

Applying this to the familiar CMU-1.svs image, QuPath + InstanSeg can detect 236,952 nuclei in 93 seconds on an M3 Max MacBook Pro with MPS acceleration.

Or 103 seconds on an Intel i7 laptop with a Quadro RTX 3000 (6GB) GPU.

[Pete Bankhead @petebankhead]

The means you can easily apply InstanSeg to whole slide images, measure & classify detections, interactively explore the results, and slot it into end-to-end analysis pipelines.

[Pete Bankhead @petebankhead]

The self-contained TorchScript also makes the method portable.

Because InstanSeg was developed using PyTorch, of course you can run it in Python.

But we’ve also written a @QuPath extension, powered by @deepjavalibrary

https://t.co/0uscfYppYU

[Pete Bankhead @petebankhead]

Let me introduce: InstanSeg 🦠🔬💻👩‍🔬

This *would* have been a short thread about Thibaut Goldsborough’s PhD work… but he solved too many problems.

Now it's a long thread about 2 preprints, a whole new approach to cell segmentation & #opensource software to make it easy to use

[African BioImaging Consortium @afribioimaging]

Join us for Episode 2 of the Community Connect Webinar Series, where Dr Sara McArdle will be giving us an introduction to QuPath and how to maximize its use in bioimaging analysis.

Don't miss out!

Click on the link to register: https://t.co/nm67ni7x3J

[Laura Nicolás-Sáenz PhD @Laura_nicolass]

Happy Friday!
Have you ever wondered why scripting in @QuPath isn’t easier? 😓
Do you want to know more about QuPath’s true aims? 🎯
I have written all about it for @FocalPlane.
Let me know what you think!

https://t.co/IKzOFvE5Jv

[Alessandro Caputo @ACaputoMD]

Glad to see #AI in #prostatecancer on the cover of the latest issue of #Pathologica (@ITA_Path) , with a picture by me & co-authors incl. @wideangle1978 & @filippofrag

p.s. Hey, that's #WSInfer + @QuPath on the cover! Shout out to @JakubKaczmarzyk & @petebankhead

[Laura Nicolás-Sáenz PhD @Laura_nicolass]

Today's video will mark a milestone in our "From Zero to @QuPath Hero" journey! 🚀 Join me later as we tackle the final available tutorial.
Are you loving the series so far? I want to hear from you! Share your feedback and let me know what you'd like to see next! #QuPathHero 📽️

[Laura Nicolás-Sáenz PhD @Laura_nicolass]

Have you seen this? Last night I posted a new video learning @QuPathª!
I have never worked with multiplexed images before and it shows 😬😬
Can you help me? or, if you are in a more competitive mood, can you do it better than me? 🧐
Join me!
#bioimageanalysis #digitalpathology

[Laura Nicolás-Sáenz PhD @Laura_nicolass]

We are getting closer to the end of the docs' tutorials and so soon we'll be sailing into more dangerous waters. ⛵️
Naturally, I would love to get some help, so if you think I am doing something wrong, or you think your approach is better, do tell!
Pete has already done so:

[QuPath @QuPath]

QuPath v0.5.1 is online! 🔍🔬

This is a minor release that parts company with a few bugs that had jumped aboard v0.5.0 🦠🐛🐞🖐️

Download it at https://t.co/AHyu02rCwn

#bioimageanalysis #digitalpathology #opensource

[Pete Bankhead @petebankhead]

@Laura_nicolass @QuPath Here's my reply to at least one of those 'why's 👨‍💻🔬👇 https://t.co/tTfnPLFwwn

[Laura Nicolás-Sáenz PhD @Laura_nicolass]

Hello future @QuPath heroes! Today I bring you a video showing how I attempt to learn Cell Classification and Density Map Creation.
Again, I get frustrated, panic, and ask "why?" a lot.
Join me! (or wait until it fully uploads in HD)
https://t.co/JFQjjGYFoA

[Pete Bankhead @petebankhead]

@Laura_nicolass @QuPath Great video! I hope other people reply / give tips / ask questions / sympathize...

I'll start: here's a video showing 5 ways to get rid of stubborn cells, some measurement table trickery, and where unlocking & editing annotations might go wrong: https://t.co/9Yb9RouB4R

[Laura Nicolás-Sáenz PhD @Laura_nicolass]

As promised, a video where I start getting frustrated while learning @QuPath

In this instalment of From Zero to QuPath Hero I try my hand at cell detection, severely mess up, 🌟panic🌟, and learn to solve a very common mistake.
Join me!

https://t.co/j9drTcbc2B