Reader @EdinburghUni. Wrote @QuPath & https://xitter.cf/t.co/eem8QmCaK8 Views my own, unless I've changed my mind. Then perhaps not even mine.
Joined January 2018
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If you want to learn about #bioimageanalysis I've written a free & open textbook that tries to help:
bioimagebook.github.io
Thanks to the wonder of @ExecutableBooks & other modern magic it's not quite like a normal book... (thread)
@OpenEdEdinburgh @NEUBIAS_COST @BioimagingNA
Pete Bankhead retweeted
Join us for the #VirtualPub with @petebankhead, University of Edinburgh, for a talk entitled "@QuPath for bioimage analysis." This talk is part of the Image Data Community Days and will be followed by the Tool Exchange with Stefania Marcotti, King's College London. Everyone is welcome to join! #ImagingCommunity
🗓️ Friday, April 11 @ 13:00 CEST
Register🔽
eurobioimaging.eu/events/ima…
Pete Bankhead retweeted
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 globias.org/activities/bia-s…
Pete Bankhead retweeted
Answering the call of @haesleinhuepf, @tischitischer,@petebankhead,@cmci_,@CiminiLab
My @FijiSc training notes are now FAIR. All online in an open format to download and use for teaching, training and other things. All in Google Doc or PDF formats
bit.ly/4hkfEBF
Pete Bankhead retweeted
📢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
Pete Bankhead retweeted
🚨 New segmentation model alert! 🚨🥳
You can finally use InstanSeg in our #BioImageAnalysis software #CellACDC!
InstanSeg is a fast and multi-channel cell segmentation model by @petebankhead, Thibaut Goldsborough, & co. The multi-channel ability is very interesting!
Pete Bankhead retweeted
We remixed holiday classics with an AI twist—check it out!
All I Want for Christmas is Digital Pathology
Frosty the Cryostat
Rockin’ Around the Scanner Tonight
Little AI Tool
Here Come the Slides
Microscopic Wonderland
AI Baby
QuPath Christmas
youtu.be/ZtxgMLZUjU4?si=87Cv…
Find out more about InstanSeg from Thibaut himself at his Virtual I2K tutorial next week!
Register at i2kconference.org/virtual.ht…
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
Pete Bankhead retweeted
Join us at the Virtual I2K meeting next week!
Lots of image analysis tutorials - including 3 about QuPath & 1 about InstanSeg 😀💻🔬
Virtual I2K starts next Monday, Oct 28!!!🎉
34 exciting tutorials on #OpenSource #ImageAnalysis
Register (for free) today!!
tinyurl.com/Virtual-I2K2024-…
Can't make it? Watch on YouTube after the event:
youtube.com/@I2KConference
2022 & 2023 tutorials available now!
ALT Flyer for Virtual I2K 2024: Online Tutorials on Image Analysis, Oct 28-30, 2024, Virtual Conference for beginners to developers. i2kconference.org for more info. Features image called Young Kelp Blades by Nat Prunet from the BINA Image Contest 2023
Second QuPath v0.6.0 release candidate now available for testing at github.com/qupath/qupath/rel…
This speeds up InstanSeg for complex annotations *and* adds much improved support to read & write OME-Zarr - @openmicroscopy
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
Pete Bankhead retweeted
"Despite repeated insistence from experts that sharing AI training data, code, and model weights [...] are necessary best practices [...], they are not universal practices among authors or publishers" Gitter et al. 🤩 osf.io/preprints/osf/2xh3w
❗️Important info hidden in the long thread❗️
Download the new QuPath v0.6.0 *release candidate* for the easiest way to try this out 💻🔬🤖
github.com/qupath/qupath/rel…
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
Pete Bankhead retweeted
I literally squeaked when I tried InstanSeg myself. I'm worried I frightened @petebankhead and Thibault Gold with my enthusiasm when I saw how good the results are. Highly, highly recommended for multiplex image analysis!!
So... Preprint #2.
In which InstanSeg is extended to output nucleus & cell boundaries - and also to handle arbitrary combinations of image input channels.
xitter.cf/petebankhead/status/18…
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
So to summarize Preprint #1:
We introduce InstanSeg as a novel nucleus segmentation method that combines state-of-the-art accuracy with being open-source, fast and portable, accelerated on different hardware, and integrated into user-friendly software.
To be continued...
...and now continued here:
xitter.cf/petebankhead/status/18…
So... Preprint #2.
In which InstanSeg is extended to output nucleus & cell boundaries - and also to handle arbitrary combinations of image input channels.
xitter.cf/petebankhead/status/18…
So... Preprint #2.
In which InstanSeg is extended to output nucleus & cell boundaries - and also to handle arbitrary combinations of image input channels.
xitter.cf/petebankhead/status/18…
So to summarize Preprint #1:
We introduce InstanSeg as a novel nucleus segmentation method that combines state-of-the-art accuracy with being open-source, fast and portable, accelerated on different hardware, and integrated into user-friendly software.
To be continued...
This bundles up QuPath & the InstanSeg extension, so it's easy* to get started.
Download it at github.com/qupath/qupath/rel…
*-Sorry non-Apple-silicon-users, GPU support can still be a pain to set up. Our attempt to help is at qupath.readthedocs.io/en/sta…
To summarize: we think InstanSeg could be pretty useful - for us & hopefully for others.
Learn more about the method at doi.org/10.48550/arXiv.2408.…
And see how it extends to multiplexed images & whole cell segmentation at
doi.org/10.1101/2024.09.04.6…
