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Hanjin Liu

@liu-hanjin.bsky.social
156 followers 107 following 20 posts

PhD in biophysics. Interested in microtubule dynamics and MAPs. Cryo-ET, fluorescence microscopy and programming. (he/him). ORCID: 0009-0006-5724-8121 github: github.com/hanjinliu

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Hanjin Liu @liu-hanjin.bsky.social · 28/09/2026
Using github.com/hanjinliu/hi... installed in native Windows to run RELION installed in WSL -- as if you are running RELION in Windows!
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Laina Hall @lainahall.bsky.social · 25/07/2026
With Cryo-ET/EM, the macromolecules we study (and biological questions we ask) are SNR-limited. Here, we share Nilas, a low-voltage milling method named after thin sea ice. Nilas produces thin (sub 50 nm in places!), minimally damaged lamellae. biorxiv.org/content/10.64898/2026.07.21.739890v1
biorxiv.org
Optimized cryo-FIB milling strategy to generate thin, minimally damaged biological lamellae
Focused ion beam (FIB)-milling has been adapted to thin frozen cells for visualization of macromolecular structures in situ with cryogenic electron microscopy. However, only a few large and abundant c...
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SBGrid Consortium @sbgrid.bsky.social · 28/06/2026
New Title Alert: miss-alignment- is a GPU-based tool for improving cryo-ET tilt-series alignments, designed to run from an initial eTomo/WarpTools patch-tracking alignment. More here: buff.ly/7mLXa49 #SBGrid #Software
buff.ly
GitHub - warpem/miss-alignment: She knows a good alignment when she sees one
She knows a good alignment when she sees one. Contribute to warpem/miss-alignment development by creating an account on GitHub.
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Wieczorek Lab @mike-wieczorek.bsky.social · 23/06/2026
New preprint! In collaboration with the Steinmetz Lab at PSI we report cryo-EM structures of microtubules at up to 1.9 Å (!) resolution & in different nucleotide state mimics, suggesting a mechanism for lattice-induced GTP hydrolysis and why it leads to catastrophe: tinyurl.com/7cjrf863
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Andrew Plested @andrewplested.bsky.social · 12/06/2026
Striking improvement with the laser phase plate to boost contrast, and in exactly the range that's needed for modelling the details of protein structures. Still lots of headroom in Cryo-EM. www.science.org/doi/10.1126/... #biophysics
Improved structural resolution for the protein haemoglobin when the laser phase plate in a cryo-electron microscope is turned on.
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bioRxiv Cell Biology @biorxiv-cellbio.bsky.social · 30/05/2026
CAMSAP2 condensates drive a γ-TuRC-independent pathway for non-centrosomal microtubule nucleation www.biorxiv.org/content/10.64898/20…
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Delnia Nazari @delnianazari.bsky.social · 28/05/2026
1/I was preparing this slide for my annual doctoral school report presentation, and I thought it was worth sharing here: For a long time, I struggled to align my cryo-ET tilts for the Golgi better, but in the end, it was unsuccessful. For some reason, even though I had good data on tomograms without
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Hanjin Liu @liu-hanjin.bsky.social · 09/05/2026
Job navigation in table view, searchable tags, 3D mesh optimized for masks, and many more features! 👉👉👉 github.com/hanjinliu/hi... Let's make our RELION directory a better place.
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Hanjin Liu @liu-hanjin.bsky.social · 03/05/2026
A little Sunday fun - syntax highlighting for STAR files and MDOC files.
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Alushin Lab @alushinlab.bsky.social · 22/04/2026
Very pleased that after a rigorous (and lengthy) review process, our paper visualizing how myosin generated forces modulate actin filament structure for mechanosensitive recogntion by α-catenin has appeared in @nature.com : www.nature.com/articles/s41...
nature.com
Myosin forces remodel F-actin for mechanosensitive protein recognition - Nature
Structural studies demonstrate that myosin generates forces that cause structural changes in actin, modulating cooperative binding by α-catenin and thus signal transduction and intercellular communica...
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Hanjin Liu @liu-hanjin.bsky.social · 20/04/2026
ChimeraX-CliX now saves up to 10,000 lines of command history, and you can quickly reverse-search commands with Ctrl+R! cxtoolshed.rbvi.ucsf.edu/apps/chimera...
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Nature Structural & Molecular Biology @natsmb.nature.com · 08/04/2026
New online: Microtubules in the axon are GDP bound but adopt a stable GTP-like expanded state
dlvr.it
Microtubules in the axon are GDP bound but adopt a stable GTP-like expanded state
Nature Structural & Molecular Biology, Published online: 08 April 2026; doi:10.1038/s41594-026-01787-7Zehr et al. revealed the 2.7-Å cryo-electron microscopy reconstruction of human microtubules in situ in the axon of induced pluripotent stem cell (iPS cell)-derived neurons. It shows an expanded microtubule lattice yet bound to GDP, in contrast to the compacted lattice observed at the iPS cell stage.
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napari @napari.org · 24/03/2026
napari 0.7.0 is available now! 🚀🎉 It's a BIG release so read the full release notes, with highlights: napari.org/stable/relea... We want to thank everyone who has worked incredibly hard on this release including our 11 new brilliant contributors 🤩 and the community for their support and feedback!
napari.org
napari 0.7.0
Mon, Mar 23, 2026 We’re happy to announce the release of napari 0.7.0! napari is a fast, interactive, multi-dimensional image viewer for Python. It’s designed for browsing, annotating, and analyzing…
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Vladimir Volkov 🇺🇦 @vladimirvolkov.bsky.social · 20/03/2026
Happy to see the first paper from the lab published in the EMBO J today: link.springer.com/article/10.1... In it, we reconstitute self-assembling cooperative oligomers of human Ndc80 and Ska kinetochore complexes that stabilise microtubule ends, and study these samples using cryoET and TIRF
link.springer.com
Microtubule end stabilisation by cooperative oligomers of Ska and Ndc80 complexes - The EMBO Journal
During mitosis, properly aligned chromosomes stabilise microtubule ends with the help of kinetochores to ensure timely segregation of chromosomes. Microtubule-binding components of the human outer kin...
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Sjors Scheres @sjorsscheres.bsky.social · 18/03/2026
We're excited to announce the beta-release of #RELION-5.1! 🥳 This release has important updates on our #amyloid processing pipeline, as described in this preprint: doi.org/10.64898/202... There are also some tweaks for #teamtomo. #OpenSoftwareAcceleratesScience
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Alushin Lab @alushinlab.bsky.social · 09/03/2026
Very excited to share our latest preprint, where we visualize the impact of force on the catch bonding actin crosslinker α-actinin-4. Led by @tri-i.bsky.social MD-PhD student Alfred Chin, a great collaboration with Glen Hocky's lab. www.biorxiv.org/content/10.6...
Images of the protein α-actinin-4 binding actin filaments in weak and strong modes, derived from cryo-electron microscopy data. Force promotes a transition from the weak mode to the strong mode, strengthening the interaction.
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Pranav NM Shah @proteincapsid.bsky.social · 24/02/2026
Just installed and twiddled a few knobs, but I am already impressed with `himena relion`. Amazing job @liu-hanjin.bsky.social! Would be great if this could be made into a default interface for relion.
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Hanjin Liu @liu-hanjin.bsky.social · 22/02/2026
Since last year, I've been making a RELION GUI that supports viewing, navigating and running jobs in a way completely compatible with the original RELION pipeline. Now it's working nicely for both SPA and tomography! Please try it out - github.com/hanjinliu/hi...
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Hanjin Liu @liu-hanjin.bsky.social · 23/12/2025
CryoEM folks, If you want to handle huge STAR file efficiently in Python, please try starfile-rs! github.com/hanjinliu/star… Reading a motion data of a particle from a 15 MB file is just like this ↓🤩
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Nico Stuurman @nicostuurman.bsky.social · 21/12/2025
One of the difficulties in developing code for microscopes is to get access to the equipment. So, wouldn't it be nice to have emulators? Turns out that AI is really good at converting documentation into an emulator: nicost.github.io/microscope-t...
nicost.github.io
Firmware Emulators
title: “Firmware Emulators for Microscope Devices” author: Nico Stuurman date: 2025-12-21 —
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bioRxiv Biophysics @biorxiv-biophys.bsky.social · 07/12/2025
Structural Basis of Human Kinetochore-Microtubule Coupling by the Ndc80 and Ska Complexes www.biorxiv.org/content/10.64898/20…
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Hanjin Liu @liu-hanjin.bsky.social · 01/12/2025
Our latest work is out in biorxiv! 😊 We show that human spastin, a microtubule severing enzyme, behaves completely differently in presence of free tubulin - it forms tubulin ring stack and promotes de novo microtubule nucleation. www.biorxiv.org/content/10.1...
biorxiv.org
Human spastin functions as an ATPase-independent microtubule nucleator via ring-stack formation
Microtubule severing enzyme spastin plays pivotal roles in cytokinesis and neuronal outgrowth, and its mutations cause hereditary spastic paraplegia (HSP). Here we show that, at physiological tubulin ...
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Sjors Scheres @sjorsscheres.bsky.social · 04/11/2025
At some point, Doppio will replace relion's gui. Already you can do more in Doppio than in relion! 🤩
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Nogales Lab @nogaleslab.bsky.social · 18/11/2025
Excited to share our new preprint in collaboration with Ahmet Yildiz's lab. Check out how our team uncovers a novel binding footprint and motor regulation mechanism for MAP9 Congrats to Burak Cetin and @aryantaheri.bsky.social www.biorxiv.org/content/10.1...
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EMBL Events @events.embl.org · 11/09/2025
Are you ready for a symposium dedicated to microtubule dynamics, function, and structure? 🙌 #EESMicrotubules will bring together researchers who share an interest in microtubule biology and its relevance to health and disease 🩺 💻 s.embl.org/ees26-09-bl ✒️ Submit your abstract by 11 March
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Vladimir Volkov 🇺🇦 @vladimirvolkov.bsky.social · 07/07/2025
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)
biorxiv.org
Microtubule end stabilisation by cooperative oligomers of Ska and Ndc80 complexes
During mitosis, properly aligned chromosomes stabilise microtubule ends with the help of kinetochores to ensure timely segregation of chromosomes. Microtubule-binding components of the human outer kinetochore, such as Ndc80 and Ska complexes, are present in multiple copies and together bind several microtubule ends, creating a highly multivalent binding interface. Whereas Ndc80:Ndc80 and Ndc80:microtubule binding is crucial for interface stability, Ndc80 alone in absence of Ska is unable to support stable kinetochore-attachments. Using cryoET, we demonstrate that oligomeric Ndc80:Ska assemblies stabilise microtubule ends against shortening by strengthening lateral contacts between tubulin protofilaments at microtubule plus-ends. We further identify a point mutation within the SKA1 microtubule-binding domain that does not affect microtubule-binding of individual Ska molecules, but does abolish Ska:Ska interactions. Finally, we report that oligomerisation of Ska, in a cooperative fashion together with the Ndc80, is necessary to maintain stable microtubule attachments both in vivo and in vitro. ### Competing Interest Statement The authors have declared no competing interest. BBSRC, BB/X014975/1, BB/W019698/1 Wellcome Trust, https://ror.org/029chgv08, 308895/Z/23/Z
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Kai Johnsson @kjohnsson.bsky.social · 03/07/2025
Finally out in Nature Chem Bio: SNAP-tag2 for faster and brighter protein labeling www.nature.com/articles/s41... Thank you Steffi and Veselin.
nature.com
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...
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Albert Dominguez Mantes @albertdm.bsky.social · 06/06/2025
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)
rdcu.be
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...
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Maxim Igaev @maxotubule.bsky.social · 03/06/2025
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.
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bioRxiv Biophysics @biorxiv-biophys.bsky.social · 27/05/2025
Cryogenic light microscopy of vitrified samples with Angstrom precision www.biorxiv.org/content/10.1101/202…
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Johannes Soltwedel @jo-soltwedel.bsky.social · 12/05/2025
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🔺:
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bioRxiv Biophysics @biorxiv-biophys.bsky.social · 05/05/2025
Enhanced axonal transport in large vertebrates: KIF5A adaptations in giraffes and pythons www.biorxiv.org/content/10.1101/202…
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Alexandre Dumoulin @axonsalex.bsky.social · 30/04/2025
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! 😉 🧪
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Hanjin Liu @liu-hanjin.bsky.social · 02/05/2025
shortest title
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napari @napari.org · 01/05/2025
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: 🧵
media.tenor.com
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!"
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napari @napari.org · 23/04/2025
napari 0.6.0rc0 is out! Barring any crazy bugs 🐛, 🙏 napari 0.6.0 should be out in a week, Apr 30.
media.tenor.com
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
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Sergio Cruz-León @sergiocruzleon.bsky.social · 11/04/2025
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
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napari @napari.fosstodon.org.ap.brid.gy · 11/04/2025
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! 🤩
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napari @napari.fosstodon.org.ap.brid.gy · 11/04/2025
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: napari.org/0.6.0/release/release_0_… But to save you a click here's a short thread: 👇
napari.org
napari 0.6.0 — napari
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Structura Biotechnology @structurabio.bsky.social · 09/04/2025
#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
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Hanjin Liu @liu-hanjin.bsky.social · 23/03/2025
3D manual picking tool along microtubules
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Hanjin Liu @liu-hanjin.bsky.social · 14/03/2025
Finally rust-numpy fully supported puthon 3.13+!! github.com/PyO3/rust-nu...
github.com
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.
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openRxiv @openrxiv.bsky.social · 11/03/2025
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
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Bose-Einstein-Kondensat @mwnautilus.bsky.social · 03/03/2025
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
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Damian Dalle Nogare @damiandn.bsky.social · 01/03/2025
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-...
forum.image.sc
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...
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Hanjin Liu @liu-hanjin.bsky.social · 01/03/2025
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.
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Hanjin Liu @liu-hanjin.bsky.social · 13/02/2025
"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 👉
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rob.mechanochemistry.org @rob.mechanochemistry.org · 12/02/2025
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.
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Malina Iwanski @mkiwanski.bsky.social · 09/02/2025
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...
biorxiv.org
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...
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Juan Nunez-Iglesias @jni.fosstodon.org.ap.brid.gy · 10/02/2025
Amazing new #Python #PEP to improve optional dependencies handling: 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! 😃
peps.python.org
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.
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