Pete Bankhead

@petebankhead

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

qupath.github.io

Joined January 2018

715 Following

3,362 Followers

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Pete Bankhead
@petebankhead
Apr 20, 2022
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
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Pete Bankhead
@petebankhead
Oct 25, 2024
Find out more about InstanSeg from Thibaut himself at his Virtual I2K tutorial next week! Register at i2kconference.org/virtual.html
Pete Bankhead
@petebankhead
Sep 11, 2024
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
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Pete Bankhead
@petebankhead
Sep 20, 2024
Second QuPath v0.6.0 release candidate now available for testing at github.com/qupath/qupath/… This speeds up InstanSeg for complex annotations *and* adds much improved support to read & write OME-Zarr - @openmicroscopy
Pete Bankhead
@petebankhead
Sep 11, 2024
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
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Pete Bankhead
@petebankhead
Sep 12, 2024
❗️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/…
Pete Bankhead
@petebankhead
Sep 11, 2024
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
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Pete Bankhead
@petebankhead
Sep 11, 2024
So... Preprint #2. In which InstanSeg is extended to output nucleus & cell boundaries - and also to handle arbitrary combinations of image input channels.
Pete Bankhead
@petebankhead
Sep 11, 2024
Replying to @petebankhead
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...
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