iiinova — where your digital self keeps evolving

Reposted by Lucien Hinderling

Ricardo Henriques @henriqueslab.bsky.social · 5h

For quantitative cell biology, the manuscript can carry its own Python or R code. Figures and reported values are rebuilt from the data at every compile, so the text stays in step with the analysis. One command also packages it for arXiv or bioRxiv 👇 rxiv-maker.henriqueslab.org

Rxiv-Maker architecture. Markdown content, Python scripts, R scripts, BibTeX references and YAML metadata feed the Rxiv-Maker processing engine, which builds a LaTeX document and figures, then outputs a publication-ready PDF and an editable Word file.

A Python code block embedded in a Rxiv-Maker manuscript. It loads monthly arXiv submission counts and computes the totals and year span that the manuscript text then quotes, so the numbers update whenever the data change.

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Ricardo Henriques @henriqueslab.bsky.social · 5h

🚀 Rxiv-Maker is now peer-reviewed and open access! Write your manuscript in Markdown and get a typeset PDF or an editable Word file, with figures, citations and cross-references numbered for you. Led by Bruno Saraiva, with @guijacquemet.bsky.social's lab 🔬 doi.org/10.1242/jcs.265183

Top of the first page of the published article 'Rxiv-Maker – an automated template engine for streamlined scientific publications' by Bruno M. Saraiva, Rita Carlota, António D. Brito, Iván Hidalgo-Cenalmor, Guillaume Jacquemet and Ricardo Henriques, showing the title, authors and abstract.

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Wolfgang Huber @wkhuber.bsky.social · 11/10/2026

This paper is on fire. Worth reading for anyone using large datasets. Question: Meng discusses population sampling and \rho_RG, the correlation between being sampled and measurement outcome. Is anyone aware of an extension to 'batch' effects, i.e. correlation between measurement error and outcome?

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Sebi @sebi06.bsky.social · 30/09/2026

Hi all, prototype of a napari-zenapi-streaming plugin is working using @zeiss-microscopy.bsky.social and @napari.org. - stream pixels from ZEN into multi-dim array and display live - stream pixels from ZEN directly into OME-ZARR (see video) For viewing I used: find-nuclei.github.io

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Estibaliz Gómez de Mariscal, PhD @gomez-mariscal.bsky.social · 18/09/2026

🚨Our work #ReScale4DL: balancing pixel and contextual information for enhanced bioimage segmentation, with @henriqueslab.bsky.social is out today!🚀 www.nature.com/articles/s41... ReScale4DL links key concepts in DL (receptive fields)+microscopy (resolution) so they can work #bettertogether😉 Threat👇

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Zach Marin @zacsimile.bsky.social · 17/09/2026

Happy to share our publication on MicroClaw, an AI agent that turns natural language requests into operations on any microscope controlled by Micro-Manager: www.biorxiv.org/content/10.6.... The software is single-click installable (download and click install.bat) at github.com/Micro-Claw/m....

biorxiv.org

Microscope control with a natural language agent

Microscopy underpins modern biology, but acquiring high-quality data from complex experiments at scale remains challenging. Smart microscopy can standardize and automate data collection, but each expe...

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Nils Norlin @nilsnorlin.bsky.social · 17/09/2026

I am looking for postdoc candidates for two opportunities in my lab at Lund University. 1. Co-application for a two-year postdoc scholarship on method development in 3D spatial biology, with applications in lung physiology, cancer and neuroscience.

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bioRxiv Biophysics @biorxiv-biophys.bsky.social · 17/09/2026

Microscope control with a natural language agent www.biorxiv.org/content/10.64898/20…

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Dave Barry @david-j-barry.bsky.social · 17/09/2026

Ah, takes me back to my postdoc days...

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Ankita Jha @ankita13jha.bsky.social · 23/08/2026

May be it only works for me but I have been using blebbing cells as calming patterns :)

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Merlin Lange @merlinlange.bsky.social · 15/09/2026

🔬🧪 We're hiring postdocs&engineers at Institut de la Vision in AMAZING Paris 🇫🇷!! Join a dynamic team working at the nexus of retina developmental biology, spatial omics & advanced imaging Ambitious science in a supportive & young inclusive team 🚀 DM me for more info & please share 🙏 #academicsky

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Lucien Hinderling @lhinderling.bsky.social · 16/09/2026

single handedly destroying academic productivity

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Anh Hoang Le, PhD 🏳️‍🌈🏴󠁧󠁢󠁳󠁣󠁴󠁿🇻🇳 @anhhle2702.bsky.social · 07/09/2026

I have 31 supp videos 😅 There will be something for everyone

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Anh Hoang Le, PhD 🏳️‍🌈🏴󠁧󠁢󠁳󠁣󠁴󠁿🇻🇳 @anhhle2702.bsky.social · 07/09/2026

4/n: Our ex vivo culture preserves the natural development as well as the natural interactions of EM cells with the surrounding ectodermal cells. EM cells often migrate in a 2.5D-3D environment and develop normally, making it suitable to study cell-cell interactions.

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Lucien Hinderling @lhinderling.bsky.social · 07/09/2026

fiber immersion 3D printing, based on the open micro-manipulator project www.youtube.com/watch?v=UvV2...

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Rob Campbell @raacampbell.com · 06/09/2026

Our BrainSaw serial-section 2-photon platform acquires whole-organ datasets automatically and requires minimal tissue processing. It has a growing international install base and has contributed to 35 publications. Learn more at: swcmicroscopy.com/brainsaw/ #microscopy #neuroscience

A BrainSaw serial section 2-photon system. This particular example was modified from an TissueCyte 1000 commercial system. Others have been built from scratch or were modified from in vivo multi-photon systems. Each BrainSaw is unique, but all run BakingTray serial section 2-photon acqusition software that plugs into ScanImage.

Somatostatin tdTomato transgenic mouse imaged on BrainSaw serial section 2-photon. Full res images acquired at around 1 micron/pixel. Top images derived from 10 micron/voxel isotropic 3D stack.

Detail from a BakingTray acquisition obtained from a BrainSaw serial section 2-photon microscope. Image shows three AAV injections leading to expression of fluorescent proteins (mCherry, GFP, and BFP) in layer 5 neurons of mouse primary visual cortex. Imaged at 780 nm.

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FocalPlane @focalplane.bsky.social · 04/09/2026

It’s #preprint list time! This week we focus on new research in bioimage analysis. Let us know if you have any suggestions for us to add to our list. focalplane.biologists.com/2026/09/04/m...

focalplane.biologists.com

Microscopy preprints: bioimage analysis - FocalPlane

Microscopy preprints: bioimage analysis - News

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Johannes Hohlbein @hohlbeinlab.bsky.social · 05/09/2026

(LinkedIn cross post) 0.12.0 of #webSMLM released. Work mainly by @kjamartens.bsky.social introduced live streaming and real time analysis from frames recorded in MicroManager or Python. hohlbeinlab.github.io/webSMLM/webS...

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Benoit Ladoux @bladoux.bsky.social · 02/09/2026

Happy to share our new study @ijmonod.bsky.social on how surface curvature shapes multicellular organization and function. How curvature controls tissue chirality, patterns distinct architectures, and influences myogenic differentiation? www.biorxiv.org/content/10.6...

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Max Farnworth @maxfarnworth.bsky.social · 31/08/2026

🚨 I AM HIRING a 3-year postdoc & 4-year PhD student 🚨 [PLEASE SHARE WIDELY] My Emmy Noether @dfg.de funded Neural Circuit & Systems Evolution lab (🌟) at the @unimainz.bsky.socialÍ wants to start existing. So..., what do we need? WELL... we need you! APPLY UNTIL 21 SEPTEMBER.

static.klipy.com

ALT:

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Giovanni D’Angelo @giodang.bsky.social · 28/08/2026

Registration is still open for the EPFL Latsis Symposium 2026, "Decoding the Cell: Modeling, Predicting, and Engineering Cellular States." 29–30 Oct, Olympic Museum, Lausanne. Quake, Haniffa, Engelhardt, Liberali, Paluch, Kundaje and more. Abstracts close 15 Sept. latsis2026.epfl.ch/event/1/

latsis2026.epfl.ch

EPFL Latsis Symposium 2026

Join us in Lausanne to connect with the global community shaping the future of cell understanding and engineering.

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Reposted by Lucien Hinderling

MwahahahahahadScientist @mads100tist.bsky.social · 29/08/2026

Do you work with microscopy images and segment to quantify or track? Do you study cell biology? development? Gather round! Let me tell you about FOCUS-3D, a segmentation algorithm that is fast, accurate and can be used on any model. We used it here to study zebrafish development. 🧪 (thread)

biorxiv.org

FOCUS‑3D: Robust, generalizable volumetric cell segmentation for three‑dimensional fluorescence microscopy

Understanding how cells establish spatial organization within tissues is a fundamental question in life sciences. While modern three-dimensional fluorescence microscopy captures large-volume tissue ar...

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Scott Brooks @scottvisionai.bsky.social · 28/08/2026

Thought I would make my bsky debut with one of my favourite NEBD movies White: NDC80-EGFP (kinetochores) Magenta: TMR::HALO-NUP107 (nuclear pores) RPE-1 cell entering mitosis on the lattice light-sheet, caught automatically by CelFDrive. #Microscopy #CellBiology #Mitosis #Science

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Richard Sever @richardsever.bsky.social · 27/08/2026

$3.7 billion spent on APCs in 2025. That's ~1000X more than it costs to run bioRxiv/medRxiv. Worth thinking about as we consider how to fund infrastructure... arxiv.org/pdf/2608.16322

arxiv.org

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Journal of Cell Science @jcellsci.bsky.social · 20/08/2026

Ali Dayoub, Alexis Gautreau, Antonina Alexandrova and colleagues investigate how two oncogenic PIK3CA mutations divergently rewire collective cell migration. Highlight: journals.biologists.com/jcs/article/... Article: journals.biologists.com/jcs/article/...

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FocalPlane @focalplane.bsky.social · 21/08/2026

We’ve just published our latest #preprint list. This week we focus on research using microscopy to answer questions in biology. Let us know if you have any recommendations for us to add to the list. focalplane.biologists.com/2026/08/21/m...

focalplane.biologists.com

Microscopy preprints: applications in biology - FocalPlane

Microscopy preprints: applications in biology - News

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Eugene Katrukha 🇺🇦 @ekatrukha.bsky.social · 17/08/2026

This manifold looks to me a lot like a bent Lorenz attractor, so I suspect this paper and data will become a treasure trove for a couple of theoretical biophysics groups. That's it, thanks for coming to my journal club, and congrats on a nice paper @micromotility.bsky.social (N/N)

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Kirsty Wan @micromotility.bsky.social · 17/08/2026

Pterosperma is a beautiful flagellate w/ 4 extremely long cilia. These cilia are so long that they can produce an entire spectrum of beating modes... To resolve the these beating patterns, we analysed >200,000 waveforms, and reconstructed the underlying manifold - strikingly low dimensional!

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Kirsty Wan @micromotility.bsky.social · 17/08/2026

What does a single-celled organism tell us about the origins of complex behaviour? Delighted to see the final version of our paper: Embodied behavioural complexity in a ciliated microorganism out in@natcomms.nature.com (Funded by @erc.europa.eu ERC) doi.org/10.1038/s414... #cilia #protistsonsky

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epithelial mechanics fan club @epimechfc.bsky.social · 16/08/2026

Tissue morphogenesis demands massive deformations, yet tissues must stay coherent. This is achieved through cell intercalation, also known as T1 transitions. But what drives them mechanically? I'm @arturruppel.bsky.social, and I'll walk you through the physics, from whole embryos down to four cells

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Joel Lüthi @joelluethi.bsky.social · 14/08/2026

We're excited to announce the 2026 OME-Zarr hackathon 🎉 📅 Date: November 2nd - November 6th 2026 📍 Location: University of Zurich, Zurich, Switzerland 💻 Virtual participation: possible for Monday afternoon, 1:00 PM CET 6:00 PM CET biovisioncenter.notion.site/2026-ome-zar... (1/6 🧵)

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Juan C. Landoni @jclandoni.bsky.social · 05/08/2026

Collecting recent-ish papers for a Cell Bio 101 course I'm teaching this fall. Ideally microscopy-driven breakthroughs that are also experimentally elegant and well written. Any favourites I should check out? 🔬

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Alana Darcher @alanadarcher.bsky.social · 30/07/2026

🎉 *extremely* excited to share our human single neuron + movie dataset is out in #ScientificData! 📄 Human neuron activity during an 83-minute movie from 2,286 neurons and 29 patients 🔗https://www.nature.com/articles/s41597-026-07955-0 1st public dataset from @humansingleneuron.bsky.social!🧵

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Beatrice Ramm @beatriceramm.bsky.social · 30/07/2026

A minimal lipid kinase/phosphatase system, two effector proteins from Legionella pneumophila, self-organizes together with its lipid substrates (PI/PI3P) into dynamic patterns on membranes. Check out our preprint: www.biorxiv.org/content/10.6...

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myosinactncrazy.bsky.social @myosinactncrazy.bsky.social · 28/07/2026

www.biorxiv.org/content/10.6... Layered helical order reveals assembly states in podosome actin networks

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Aafke Gros @aafkegros.bsky.social · 24/07/2026

Microscopy Nodes 3.1 is out for Blender 5.2! 🎉 This has cool new features for conditional masking, working with even larger data (regional upscaling), and data manipulation! Watch the new youtube tutorials that explain the features: www.youtube.com/playlist?lis...

A FIB-SEM plankton visualization where the top shows only the volumetric data of the chromosomes, and the bottom a normally sliced region of the cell.

A fluorescence microscopy dataset where a region has been reloaded to be much higher resolution

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Joel Lüthi @joelluethi.bsky.social · 24/07/2026

Do you want to learn more about OME-Zarr viewers, where they stand today and what's being developed at the moment? On August 24th at 4pm CEST, we will hear about 3 different OME-Zarr viewers and user stories for each. www.biovisioncenter.uzh.ch/en/events/Up... (1/5 🧵)

biovisioncenter.uzh.ch

Open Bioimaging Practices Meetup August 2026

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Lucien Hinderling @lhinderling.bsky.social · 24/07/2026

phone based photogrammetry/splatting is not precise enough?

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jared toettcher @toettch.bsky.social · 24/07/2026

I should also point out that there are other *excellent* steps in the "smart microscopy" + optogenetics direction, including recent efforts by the Pertz and Kapitein labs, that are reviewed here. Take a look! www.degruyterbrill.com/document/doi...

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jared toettcher @toettch.bsky.social · 24/07/2026

New Toettchlab paper alert! Harrison Oatman just published his beautiful work combining software design for "smart" microscopy+optogenetics and some really beautiful work understanding EGFR-driven collective cell migration. www.cell.com/cell-systems...

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Wolfgang Huber @wkhuber.bsky.social · 23/07/2026

Optogenetics equivalent of the "IBM written in atoms" AFM image: hinderling.github.io/assets/pertz... (from hinderling.github.io)

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Kate Cavanaugh @katecavanaugh.bsky.social · 01/10/2025

See this? This = implanting mouse embryo. Usually this happens inside its mother and is invisible to us, but we can actually watch implantation ex vivo with the hope of understanding why implantation goes awry in embryos of older women. A 🧵...

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Teng-Leong Chew @scopeshifu.bsky.social · 15/07/2026

🧪 @aicjanelia.bsky.social and @scientistrachel.bsky.social have just published a new quantitative tool, OpticalFlow3D, for tracking amorphous motion in 3D. Try it out and let us know what you think! tinyurl.com/OpticalFlow3D

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Mario Del Rosario @mariodelr.bsky.social · 05/06/2026

How do you know if a microscopy experiment can actually resolve a biological structure? Introducing VLab4Mic, a platform that predicts structural resolvability before you go to the microscope Led by Damián Martinez and Bruno Saraiva at @henriqueslab.bsky.social www.biorxiv.org/content/10.6...

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epithelial mechanics fan club @epimechfc.bsky.social · 12/04/2026

How does an orbiting spherical tissue suddenly break symmetry and sprout invasive strands? We can predict this behavior from the initial morphology! Hi, I’m @jiwon-kim.bsky.social from @ianywonglab.bsky.social.

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Jiwon Kim @jiwon-kim.bsky.social · 12/04/2026

Our thread is now up at @epimechfc.bsky.social 💗 Take a look if you are interested in how a living tissue knows how to sculpt itself!

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epithelial mechanics fan club @epimechfc.bsky.social · 03/05/2026

How do epithelial cells integrate mechanical and biochemical signals to control their behavior? I am @ronjahoutekamer.bsky.social, and in this thread, I’ll show you how force transduction connects to biochemical signaling, and how it activates ERK by inducing biochemical ligand shedding.

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