#Mastodon, the Command Center for Large-Scale Lineage-Tracing Microscopy Datasets, is finally heading for publication (well, let's see). To #cite or not to cite shall no longer be the question 🙃, because the #preprint. Software is available in every #Fiji near you.

www.biorxiv.org/content/10.6...

October in preprints - the Node Welcome to our monthly trawl for developmental and stem cell biology (and related) preprints. The preprints this month are hosted on bioRxiv.

You must have been looking forward to... October in preprints!

Check out the latest #preprints on #DevBio, #StemCell biology and related topics with, starting this month, @prelights.bsky.social picks 👇👀

thenode.biologists.com/october-in-p...

Do you love the monthly #preprint lists on @the-node.bsky.social?

Good news, our #preLighters have teamed up with the Node to nominate standout articles and share one-paragraph insights on why they’re excited.

Check out their October highlights ⬇️ 👀
thenode.biologists.com/prelighters-...

Really excited to present the results of a fantastic collaboration with Jesse Veenvliet @jesseveenvliet.bsky.social @mpi-cbg.de @poldresden.bsky.social 🤩

We find a unique mechanism for body axis elongation in mammals, different from other vertebrate species

➡️ www.biorxiv.org/content/10.1...

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 🧵...

September in preprints – Cell biology edition - preLights

Happy October 1st!

A good time to share another #CellBio #preprint reading list put together by a team of preLighters: @sristi.bsky.social, Matthew Davies, @vibhasingh.bsky.social, @fadelvalle.bsky.social & Barbora Knotkova.

Check out their picks ⬇️👀
prelights.biologists.com/prelists/sep...

Mechano-osmotic signals control chromatin state and fate transitions in pluripotent stem cells - Nature Cell Biology McCreery, Stubb et al. show that mechano-osmotic changes in the nucleus induce general transcriptional repression and prime chromatin for cell fate transitions by relieving repression of specific differentiation genes.

How do #stemcells integrate information to coordinate fate decisions? Delighted to finally see our work showing how growth factors regulate the mechano-osmotic state of the #nucleus and #chromatin to control #pluripotency exit out! www.nature.com/articles/s41... see 🧵 👇

Tissue 'tectonic' collision is detrimental, but flies found two distinct solutions! Gratifying and grateful to be included in this collective effort, w/ Steffen Lemke, to crack the (or 'a') code of #cephalicfurrow, now out in @nature.com, all with @paveltomancak.bsky.social at the helm. (1/9)

Our latest preprint! Into morphogenesis, Yap, ECM, signaling, vertex models, feedbacks/robustness? There is something here for everyone. We discovered a positive feedback loop that extends inner ear canals, and a built-in mechanism that shuts it down when morphogenesis is done. tinyurl.com/464wsjhd

Integrating Tissue and Cytoplasmic Rigidity Transitions During Morphogenesis Multicellular organisms generate organizational complexity through morphogenesis, in which mechanical forces orchestrate the movements and deformations of cells and tissues, while chemical signals re...

Excited to share our new review in Development, Growth and Differentiation(DGD) Journall!

With the amazing @yuchiunwang.bsky.social & @bipashadey29.bsky.social,we explore how rigidity transitions bridge cytoplasmic & tissue scales.

Read the full review: onlinelibrary.wiley.com/doi/full/10....

Capillary constrictions prime cancer cell tumorigenicity through PIEZO1 - preLights Cancer cells that survive, thrive: capillary constrictions as a trigger of mechanotransduction in cancer progression

Cancer cells that survive, thrive: capillary constrictions as a trigger of mechanotransduction in cancer progression.

Check out this #preLight by Sristilekha Nath, which talks about the work by @gsilvani.bsky.social, @kriskilian.bsky.social and the team.

From genes to patterns: five key dynamical systems concepts to decode developmental regulatory mechanisms Summary: Dynamical systems theory provides a powerful quantitative and intuitive framework to understand developmental processes. This Primer brings key concepts of this framework to the ever-growing ...

A Summer reading recommendation: new primer in @dev-journal.bsky.social explains how dynamical systems theory unlocks the logic of developmental patterning

Everything from bistable switches & oscillators to phase portraits & more with Python code to explore

journals.biologists.com/dev/article/...

CellPhePy: A python implementation of the CellPhe toolkit for automated cell phenotyping from microscopy time‐lapse videos We previously developed the CellPhe toolkit, an open-source R package for automated cell phenotyping from ptychography time-lapse videos. To align with the growing adoption of python-based image anal...

CellPhePy is now available 🎉🎉🎉 in the journal of #microscopy. A python version for #CellPhe.
See doi.org/10.1111/jmi....
Thanks @ukri.org and @wellcometrust.bsky.social for funding

@globias.bsky.social @globalbioimaging.bsky.social @eurobioimaging.bsky.social @bioimaginguk.bsky.social

Happy to share our new preprint on lens morphogenesis in ocular organoids. All thanks to Elin Stahl, Miguel Angel Delgado-Toscano, Ishwariya Saravanan, Anastasija Paneva and Jochen Wittbrodt @wittbrodtlab.bsky.social

www.biorxiv.org/content/10.1...

Interplay of actin nematodynamics and anisotropic tension controls endothelial mechanics Nature Physics - Blood flow through a vessel deforms vessel walls. Cells lining these walls sense the changes in pressure as blood flows and reorient their actin fibres in the direction of largest...

Very happy and excited to share our latest work linking actin nematodynamics and endothelial cell mechanics under anisotropic tension, now published in @natphys.nature.com ! rdcu.be/eigWi

@ipparis.bsky.social @polytechniqueparis.bsky.social

March in preprints – the CellBio edition - preLights

It’s about time to share the March #CellBio preprint picks!

8 preLighters (@girishkalephd.bsky.social, @fadelvalle.bsky.social, @ethanewe.bsky.social, @sristi.bsky.social, @vibhasingh.bsky.social, @deevithab.bsky.social) teamed up to curate this #preList ⬇️

prelights.biologists.com/prelists/mar...

Tissue-like multicellular development triggered by mechanical compression in archaea The advent of clonal multicellularity is a critical evolutionary milestone, seen often in eukaryotes, rarely in bacteria, and only once in archaea. We show that uniaxial compression induces clonal mul...

Striking new study from @archaeon-alex.bsky.social's lab just out in @science.org on multicellular development induced by compression in Archaea: www.science.org/doi/10.1126/...

The more jargon you have in your paper the less citations you'll get.
royalsocietypublishing.org/doi/10.1098/...

3D reconstruction of a 3-day-old #zebrafish heart beating. Credit to Michael Weber (prev. @mpi-cbg.de). #ZebrafishZunday 🧪

A duo of preprints on the dynamics of the first cell fate decision in mouse by Madeleine Chalifoux (first grad student in the lab!) and Maria Avdeeva (Flatiron).

We use quantitative live imaging of key cell fate determinants to follow the segregation of inner cell mass and trophectoderm lineages.

This CellBio #preList is yet another great team effort! #community #ECRs

Many thanks Barbora, Matthew, @sristi.bsky.social , @girishkalephd.bsky.social, Prasanna, Vibha & @fadelvalle.bsky.social for putting it together! 🙌 #preLighters

Check out our latest podcast episode ( #spotLights ) in which we talk to the creator of #tidyplots: Jan Broder Engler🎙

Ep. 7 🎧: www.youtube.com/watch?v=o0kl...

Also, please take a look at the related #preLights post prepared by Felipe Del Valle Batalla: prelights.biologists.com/highlights/t...

Measuring plasma membrane fluidity using confocal microscopy - Nature Protocols Membrane fluidity is a crucial feature in understanding cellular physiology. This protocol describes a robust pipeline for measuring plasma membrane fluidity using confocal imaging and new environment...

New paper out 🎇
It has been 13 years since @owenlabuob.bsky.social and co. published a stellar protocol on how to measure membrane order with smart probes! Since then, there has been new dyes, imaging modes and biology! We wrote a protocol for Nature Protocols:
www.nature.com/articles/s41...

Here it is, in collaboration with @lankylaste.bsky.social, Lina Gerontogianni & Gavin Kelly: www.biorxiv.org/content/10.1...

* Stats tests often used inappropriately
* Masses of data points are often unnecessary
* Inferring biological significance almost impossible without appropriate controls

Deforming Nuclei: a way to move through the crowd! - the Node In their recent paper, Maia-Gil and colleagues explored whether and how nuclear properties can influence nuclear positioning in vivo. Their work revealed

Deforming Nuclei: a way to move through the crowd!

Read this #BehindthePaper story from Mariana Maia-Gil about the work @nordenlab.bsky.social, looking into how nuclear properties influence nuclear positioning in the densely packed🐟retinal neuroepithelium:
thenode.biologists.com/deforming-nu...

January in preprints – the CellBio edition - preLights

📃January in preprints – the CellBio edition

This latest cell biology #preList was curated by Barbora Knotkova, Vibha Singh, Matthew Davies, @fadelvalle.bsky.social and @girishkalephd.bsky.social

Explore their favourite #CellBio #preprints!

⬇️

Microscopy preprints - bioimage analysis - FocalPlane Microscopy preprints - bioimage analysis - News

Check out our latest #preprint list on FocalPlane. This week we focus on bioimage analysis tools and their application to biological images.
focalplane.biologists.com/2025/01/24/m...

Explanation in Biology Cambridge Core - Philosophy of Science - Explanation in Biology

Years ago I had several philosophy of science questions that are clearly addressed in this book www.cambridge.org/core/element... great to read!

Yamini @yamini-ravichan.bsky.social changed the topology of Hydra to show that actin orientational defects of Hydra induce the full program of head regeneration: www.science.org/doi/10.1126/...
Mechanics controls development! Thanks to Dan Pearce, Karsten Kruse, Matthias Vogg & Brigitte Galliot.

FIB-SEM dataset visualized with Microscopy Nodes, data from Mocaer et al 2023

Microscopy Nodes is now up on bioRxiv! 🚀

This is a Blender extension that seamlessly integrates and visualizes 3D microscopy data (TIF & @zarr.dev).

High-quality volume rendering for anyone, in both EM and fluorescence, regardless of computational expertise! 🔬

www.biorxiv.org/content/10.1...