Pete Bankhead

Reader @EdinburghUni. Wrote @QuPath & my own, unless I've changed my mind. Then perhaps not even mine.

[Pete Bankhead @petebankhead]

If you want to learn about #bioimageanalysis I've written a free & open textbook that tries to help:
https://t.co/VNdOzY3AYP

Thanks to the wonder of @ExecutableBooks & other modern magic it's not quite like a normal book... (thread)

@OpenEdEdinburgh @NEUBIAS_COST @BioimagingNA

[Euro-BioImaging ERIC @EuroBioImaging]

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🔽
https://t.co/eNjznKEugp

[Pete Bankhead @petebankhead]

@bio_leon @QuPath We have instructions at https://t.co/hPmy2lix4P but they need updated as macOS changes... in Sequoia, I get a 'Not Opened' error - but under 'Privacy & Security' in System Settings I see an option to 'Open Anyway'. Not easy to find, but only required the first time QuPath runs.

[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

[Cameron Nowell @NerdyCammy]

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

https://t.co/Dp3YrJPbGp

[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

[Francesco Padovani @frank_pado]

🚨 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!

[Matthew Cecchini MD PhD FRCPC @Path_Matt]

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

https://t.co/tsHmHTfe5p

[Pete Bankhead @petebankhead]

Find out more about InstanSeg from Thibaut himself at his Virtual I2K tutorial next week!
Register at https://t.co/iEVjaZ9I3k

[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

[QuPath @QuPath]

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

[Pete Bankhead @petebankhead]

Second QuPath v0.6.0 release candidate now available for testing at https://t.co/j4w5C2czBU

This speeds up InstanSeg for complex annotations *and* adds much improved support to read & write OME-Zarr - @openmicroscopy

[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

[Robert Haase @haesleinhuepf]

"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. 🤩 https://t.co/gxkZZcNlj5

[Pete Bankhead @petebankhead]

@ajinkya_talks What you need depends on which model you use - check out the thread & preprints for examples & answers

[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

[Pete Bankhead @petebankhead]

@Kingsley2019 @dannygazali It's nothing something we're working on (or know very much about) but the topic has come up on the forum a few times:
https://t.co/gnuVzlfnG3

Since QuPath open-source & others can modify/extend it, many things may be possible without us knowing about them or being involved :)

[Pete Bankhead @petebankhead]

@lgamon @QuPath So do we! We rely on @bioformats for that though. Only thing that might help slightly in QuPath v0.6 is initial read/write support for OME-Zarr, so maybe converting sometimes could help... (although still have to figure out how best to handle metadata)

[Pete Bankhead @petebankhead]

@BoSoxBioBeth Intrigued!

[Pete Bankhead @petebankhead]

❗️Important info hidden in the long thread❗️
Download the new QuPath v0.6.0 *release candidate* for the easiest way to try this out 💻🔬🤖
https://t.co/S6aFegoUVX

[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

[Pete Bankhead @petebankhead]

@dannygazali By far the easiest way to try it out is with the new QuPath release candidate: https://t.co/owr19HoYw3
With DeepImageJ, you might need to do a bit more preparation (the main thing is resizing your image to have a pixel size close to 0.5µm) - but it's automatic in QuPath.

[Pete Bankhead @petebankhead]

This bundles up QuPath & the InstanSeg extension, so it's easy* to get started.

Download it at https://t.co/S6aFegoUVX

*-Sorry non-Apple-silicon-users, GPU support can still be a pain to set up. Our attempt to help is at https://t.co/8KGLWSswEP

[Sara McArdle @SaraMcArdle1]

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!!

[Pete Bankhead @petebankhead]

@hariharmm We haven't tried - but if there's a good public dataset for training, we could give it a go!

If not, a discussion on https://t.co/rFYWNLQPyc could be a good place to try to figure it out.