Hanjin Liu

New preprint from the lab - the first paper made (almost) entirely here @qmul.bsky.social

We report how human outer kinetochore complexes Ndc80 and Ska form cooperative oligomers, that together stabilise microtubule ends against shortening.
www.biorxiv.org/content/10.1...

Key results below: (1/7)

SNAP-tag2 for faster and brighter protein labeling - Nature Chemical Biology SNAP-tag is a widespread tool for labeling protein for bioimaging. Now, Kühn et al. report SNAP-tag2 with increased labeling kinetics and brightness, which translates into a better performance in live...

Finally out in Nature Chem Bio:
SNAP-tag2 for faster and brighter protein labeling
www.nature.com/articles/s41...
Thank you Steffi and Veselin.

Spotiflow: accurate and efficient spot detection for fluorescence microscopy with deep stereographic flow regression Nature Methods - Spotiflow uses deep learning for subpixel-accurate spot detection in diverse 2D and 3D images. The improved accuracy offered by Spotiflow enables improved biological insights in...

Spotiflow, our deep learning based spot detection method for microscopy, is now published in @natmethods.nature.com!
Since the pre-print, we have added many features, notably native 3D detection!
@maweigert.bsky.social @gioelelamanno.bsky.social @epfl-brainmind.bsky.social
Paper: rdcu.be/epIB7
(1/N)

Excited to share our latest work in @pnas.org! Combining simulations and cryo-ET, we reveal how microtubules decide between growth and shortening. doi.org/10.1073/pnas... @maksimkalutskii.bsky.social @vladimirvolkov.bsky.social @compbiophys.bsky.social @mpi-nat.bsky.social @qmul.ac.uk @dundee.ac.uk.

Cryogenic light microscopy of vitrified samples with Angstrom precision https://www.biorxiv.org/content/10.1101/2025.05.27.656160v1

New release: napari-omero 0.5.0 😀@openmicroscopy.org @napari.org thanks to some big contributions from @psobolewskiphd.bsky.social , @will-j-moore.bsky.social and of course @talley.codes. Some features in spotlight 👇

First: napari-omero now supports lazy loading of image pyramids from OMERO🔺:

Enhanced axonal transport in large vertebrates: KIF5A adaptations in giraffes and pythons https://www.biorxiv.org/content/10.1101/2025.05.04.652084v1

This time-lapse captures 17 hours of axonal growth from a chicken dorsal root ganglion explant, visualized through the actin cytoskeleton using live confocal imaging.
I just submitted this video to the Nikon Small World in Motion competition. Today is the last day to upload yours! 😉
🧪

shortest title

a woman in a hat is crying and says " i 've traveled a good many miles to get here " Alt: Charlotte from the Sanditon TV series, emotionally exclaiming, "I've traveled a good many miles to get here!"

And it's finally here! napari 0.6.0 is out on PyPI and conda-forge! 🥳 We've had a few threads about this release already but let's recap with some highlights: 🧵

doctor strange says we 're in the endgame now in a movie scene Alt: Doctor Strange says "we're in the endgame now" in a scene from Avengers: Infinity War

napari 0.6.0rc0 is out! Barring any crazy bugs 🐛, 🙏 napari 0.6.0 should be out in a week, Apr 30.

Excited to share our preprint on the molecular architecture of heterochromatin in human cells 🧬🔬w/ @jpkreysing.bsky.social, @johannesbetz.bsky.social,
@marinalusic.bsky.social, Turoňová lab, @hummerlab.bsky.social @becklab.bsky.social @mpibp.bsky.social

🔗 Preprint here tinyurl.com/3a74uanv

Thanks to Hanjin Liu, napari now has a command palette! 🎨 This thing is really nice to use — the core team can no longer live without it — and it even works with plugin commands! 🤩

It's taking us some time but it's gonna be worth the wait we promise! 😅 napari 0.6.0a1 is out now! You can install it with `pip install "napari>=0.6.0a1"`. The full release notes are here:

https://napari.org/0.6.0/release/release_0_6_0.html

But to save you a click here's a short thread: 👇

#CryoSPARC v4.7 is out! 🚀 
Featuring a new automatic Micrograph Junk Detector that labels and rejects contaminants, new tools for curating subsets of particles, performance and stability fixes, and more!
Full changelog: cryosparc.com/updates

#cryoEM

3D manual picking tool along microtubules

GitHub - PyO3/rust-numpy: PyO3-based Rust bindings of the NumPy C-API PyO3-based Rust bindings of the NumPy C-API. Contribute to PyO3/rust-numpy development by creating an account on GitHub.

Finally rust-numpy fully supported puthon 3.13+!!

github.com/PyO3/rust-nu...

openRxiv has arrived!

We’re thrilled to announce the launch of openRxiv as an independent, researcher-led nonprofit to oversee bioRxiv and medRxiv, the world’s leading preprint servers for life and health sciences.
openrxiv.org/introducing-...

#openRxiv #OpenScience #Preprints #bioRxiv #medRxiv

Customizable large-scale #OpenSource #HPLC #FractionCollector using low-cost #3Dprinting:

- based on #Creality #Ender3Pro
- cost < US $280
- prep scale fractions: up to 470 mL
- #Python, #GUI, no-code

doi.org/10.1016/j.oh...
#DIYbio #lab #instruments #LC #fluidics #chemistry #DrugDiscovery

Fiji 2024 Year in Review: Milestones and Roadmap Introduction The Fiji team at LOCI is pleased to share significant progress on several major initiatives as we work towards raising the technological standards of Fiji. These include Fiji 2.16.0, feat...

Wow, this is big: "Fiji can now be launched in a Python-first mode, where first Python is started, then Fiji is started via the PyImageJ library. In this mode, Fiji is fully integrated with the active Python environment"
forum.image.sc/t/fiji-2024-...

Even though I don’t usually use it, I cannot emphasize more how much ImageJ is educational. It is a great tool to show students how image processing and image analysis works.

"himena" is an *infinitely extensible* application for data science I made recently.

github.com/hanjinliu/hi...

You can open any data, integrate any widget, and your plugin will look as if it is a built-in function.
Attached GIF shows my own plugin "himena-image" for image analysis 👉

Yean Ming Chew and I wrote doi.org/10.1042/BST2... about MT lattice switching. We discuss evidence that protofilament-level structural switching is ancient and fundamental and conserved; and that tubulation creates new allosteric interfaces that operate on essentially the same structural switch.

Polarity reversal of stable microtubules during neuronal development Neurons critically depend on long-distance transport orchestrated by motor proteins walking over their highly asymmetric microtubule cytoskeleton. These microtubules are organized uniformly in axons w...

My main PhD paper is on bioRxiv! 🥳 We used motor-PAINT, expansion microscopy, and live-cell imaging of StableMARK to map out how the microtubule cytoskeleton reorganizes during neuronal development.
www.biorxiv.org/content/10.1...

PEP 771: Default Extras for Python Software Packages PEP 508 specifies a mini-language for declaring package dependencies. One feature of this language is the ability to specify extras, which are optional components of a distribution that, when used, install additional dependencies. This PEP proposes a mechanism to allow one or more extras to be installed by default if none are provided explicitly.

Amazing new #Python #PEP to improve optional dependencies handling:

https://peps.python.org/pep-0771/

The PEP is very thorough and well-written, and it perfectly uses @napari as a motivating example. We were not involved but we fully endorse it! 😃

Hi ChimeraX users!
CliX, the intelligent command line interface, now works very nicely with the system dark theme!

Check it out -> cxtoolshed.rbvi.ucsf.edu/apps/chimera...

From napari to the world: how we generalized the `conda/constructor` stack for distributing Python applications Our work for the napari project resulted in multiple beneficial side effects for the conda packaging ecosystem.

📦 Packaging Python apps just got easier! @rjai.me 's latest #QuansightLabs blog explores how napari's team reimagined installers, creating tools that benefit the entire scientific computing community. https://buff.ly/4jMCZxx 🔬 #OpenSourceInnovation

We are pleased to introduce the newest members of the JCB Editorial Board: Anna Akhmanova, @msubrandizzilab.bsky.social, @goleylab.bsky.social, @christlet.bsky.social, @olzmannlab.bsky.social, Marisa Otegui, Christian Ungermann, Chonglin Yang, and Yan Zhao. https://buff.ly/3Q1O0NT

Diverse microtubule-binding repeats regulate TPX2 activities at distinct locations within the spindle Liang et al. elucidate that TPX2 possesses α-helical repeats exhibiting opposite preferences for “extended” and “compacted” tubulin dimer spacing, with the

rupress.org/jcb/article-...

Best way to start 2025! Thrilled to share our Nature paper about the structures of axonemal components from sperm flagella and from epithelial cilia of the oviduct and brain ventricles. Great collaboration with Tzviya Zeev-Ben-Mordehai and @alanbrownhms.bsky.social

www.nature.com/articles/s41...