We tracked a zebrafish tail tip for 30h of light-sheet imaging.
It didn’t exist at t=0.
LiLiTTool: CoTracker3 + object detection → real-time microscope steering.
3D, multi-ROI, open source.
www.biorxiv.org/content/10.6...
#bioimaging #lightsheet
thanks @jytinevez.bsky.social
🤩
🎉 ggauto is now on CRAN 🎉
An #RStats package that selects better chart types, and provides more accessible styling for #ggplot2 plots 📊
Blog post explaining why I made it and how it works: nrennie.rbind.io/blog/introdu...
#DataViz
Mechanisms of active wetting and fluidification in epithelial cell collectives
go.nature.com/3Pxjq1E
Are you interested in the Cell Painting Assay but have some questions? We've curated a whole bunch of resources into a comprehensive and friendly "Cell Painting for Biologists" guide ciminilab.github.io/GuideToCellP...
Fig. 1. Force impact on embryogenesis and organogenesis. Compelling evidence from published reports demonstrates that fate and differentiation of embryonic stem cells and adult stem cells depend on forces (shear and/or normal stress), substrate elasticity/viscoelasticity, and substrate topography. The observation from cell culture studies that mesenchymal stem cells undergo neurogenesis on soft substrates is consistent with the finding that a stiffness gradient is responsible for axons to change their turning direction caudally towards soft tissues in the developing Xenopus embryonic brain in vivo. Stem-cell based models are useful in understanding role of forces in the development of embryos, which are inaccessible in vivo for mammalian embryos. Blastoid formation via iPSCs is enhanced by 3D culture and substrate mechanics and may depend on endogenous forces (endo-force). Maturation of cardiomyocytes from iPSC differentiation is promoted by mechanical stretching. iPSC, induced pluripotent stem cells. Force is used here generically to represent any type of mechanical loading (force, torque, tensile or compressive stress, shear stress, torque per volume or specific torque) (exogenously or endogenously).
Fig. 2. A mechanobiology model of tumor cell self-renewal and metastasis. Matrix metalloproteinases (MMPs) from the primary tumor site soften the extracellular matrix (ECM) of the tumor microenvironment and break tumor cell dormancy, leading to tumor cell invasion. Stiff (>800 Pa) differentiated tumor cells and soft (<300 Pa) undifferentiated tumor stem cells such as tumor-repopulating cells (Lv et al., 2020) enter blood vessels (intravasation), arrest at narrow vessels, and exit blood vessels (extravasation) to metastasize to distance sites and form micrometastasis. In some cases, soft tumor stem cells proliferate and self-renew within a soft matrix (e.g., bone marrow, brain, lung, and liver) to establish metastatic colonization and grow into macroscopic metastases, or survive and enter dormancy within the stiff matrix, whereas stiff differentiated tumor cells die in the soft or stiff matrix of a different tissue (denoted by an X). In some other cases, when the matrix of tumor microenvironment of metastatic sites becomes inflamed and then softened, soft dormant tumor stem cells will exit dormancy, self-renew, and grow into clinically-detectable macroscopic metastases. Note that this simple model illustrates an element of the Virchow's postulate and highlights softness-based mechanoregulation of cancer progression, which is also regulated by other physical and soluble factors and cells such as tumor-associated fibroblasts and immune cells.
Fig. 3. Cell softness regulates cytotoxic T cell killing of tumor cells. Cytotoxic T cells enter tumor parenchyma, where the T cells use T cell receptor (TCR) to recognize MHC (major histocompatibility complex)-tumor antigenic peptide complex and form the synapse. The activated T cells then release perforin and granzymes to the synapse space where perforin forms pores on the plasma membrane of target tumor cells and allows the entry of granzymes into the cytoplasm, activating caspases 3 and 7 and leading to tumor cell apoptosis. However, drilling pores by perforin is not only a chemical but also a mechanical process. Cell stiffness (>600 Pa) is required for the pore formation by perforin and cell softness impairs perforin pore formation. Thus, soft (<300 Pa) tumor stem cells such as tumor-repopulating cells use their softness to evade T cell cytolysis by impeding perforin pore formation. On the other hand, activated T cells might be very soft, avoiding autolysis. In addition, it is possible that TCR-MHC binding may be equal in the molecular number but the interacting force may be weaker between the soft tumor cell and the immune cell than between the stiff tumor cell and the immune cell; as a result, the released granzyme and perforin from the immune cell may be less, contributing to less killing of the soft tumor cell. Stiff target cells are engulfed more avidly than soft target cells by macrophages, suggesting that this model may be applied to other immune cells.
Some say development is guided by forces. While the role of chemistry in dev bio is undeniable, growing evidence has pointed out the significant contribution of physics too. Chowdhury et al discuss how forces shape normal and cancer stem cells and the clinical applications.
doi.org/10.1016/j.cd...
Looks amazing and needed 🤩
Optical clearing & time-lapse fluorescent imaging of Live mouse Brain (up to 800 μm of depth)🤯
An acute olfactory bulb slice(P11) loaded with GCaMP6f (Ca2+ sensor) was imaged with #2PM at a depth of 150 μm during clearing with SeeDB-Live👹
#NatMethods 2026
www.nature.com/articles/s41...
ECM swelling pressure driving morphogenesis. Tumours can also accumulate high HA and cause pressure, I wonder how general this mechanism is across tissues.
pubmed.ncbi.nlm.nih.gov/34942099/
We had covered the history of traction force microscopy (TFM) earlier:
bsky.app/profile/epim...
But what about applying TFM into more physiologically relevant systems, such as those in 3D?
I am @barrasa-fano.bsky.social and I'll be your guide through this thread on #3DTractionForceMicroscopy.
We summarised the many roles of material phase transitions in development (and they are not just mechanical 🤔)
One on left is a black dog and above it the words “Reality”. Below it is “I chased a squirrel” One the right is a black dog and above it says “LinkedIn”. Below it says, Proud to announce that I effectively executed a rapid-response squirrel displacement strategy to mitigate potential yard intrusions. Humbled by the unwavering support of my family and local stakeholders. This experience reinforced the importance of vigilance, ownership, and continuous improvement. Looking forward to scaling this impact in future engagements.
😂
Hello epithelial mechanics fans!! I’m Juanma @juanmagararc.bsky.social 👋 I work on cell mechanics (see celldynamicslab.com) and use Flipper-TR FLIM to probe membrane biophysics in cells.
Join me on this tour about Flipper: what it measures, strengths, advice, cool case studies, and cute drawings!
@marineluciano.bsky.social recreates intestinal Villi geometry by growing epithelial cells on wavy rolling substrates. Unexpected intrication of curvature effects is observed. Thanks to all! @caterinatomba.bsky.social @sgabriele.bsky.social @sciencesunige.bsky.social
www.biorxiv.org/content/10.6...
Following on from her beautiful featured image post on FocalPlane, Christina Daly @christinaadaly.bsky.social shares her top tips for imaging cytonemes.
@labogden.bsky.social.
focalplane.biologists.com/2026/01/19/c...
Dimensionality of cell migration.
Cells can move along 1D tracks, in 2D sheets, confined between a hard surface and fluid (2.5D), and within a 3D tissue.
Pick the optimal cell migration assay for your application using our review paper here:
www.nature.com/articles/s41...
How can structures at the vertex of 3 cells have effects at the tissue level?
Join me, @laura-rustarazo.bsky.social, to explore how tricellular junctions (TCJs) act as local tension sensors and regulators of global tissue organization. 🧵⤵️ doi.org/10.1126/scie...
Photograph from 1911 taken by Herbert Ponting whilst with Scott's Antarctic Expedition The monochrome photo is taken from within a cave. The walls of the cave are made of ice. The cave entrance is in the mid distance with two figures standing looking out towards a distant ship. Between them and the ship there is first a 'beach' of ice before the sea itself. The ship could be up to 800 metres away What makes the photo so special is that where the figures are at the cave entrance there is a band of very white snow and ice (contrasting with the comparatively dark inside of the cave) that creates a stark framework in which the men and the ship are captured. It is made even more dramatic by the fact that the cave entrance is at least 30 metres high and is in the shape of a distorted elipse with the tail sloping off to the right at the top of the elipse The photo being in monochrome in a largely white environment makes the photographers skill all the more laudable
This photo was taken in 1911 using glass plate technology by Herbert Ponting who was part of Scott's Antarctic expedition,
The composition and detail are exquisite with the band of white snow/ice creating a perfect frame around the two people and the ship in the distance
Iconic imo
New year, new beginnings! Join us for all things animal & plant devbio at the 2026 @bsdb.bsky.social meeting in Warwick!
Abstract submission closing NEXT FRIDAY 16th JAN - join us!
I'll be presenting about "Breaking Biological Barriers" at Night Science Seminar Series on 12 Jan. I'll also try to say some things you don't normally hear people say about the academic process... cassyni.com/events/TjxgV...
📣Registration deadline approaching !📣
Check out @embo.org @biologists.bsky.social workshop "biophysical & molecular mechanisms of animal homeostasis & repair" 6-10th April, with a fantastic lineup of speakers! meetings.embo.org/event/26-hom....
Register/Abstract submission by 10th January.
מלטונין, שוקולד וחשיפה לשמש
A thorough review of deep-learning approaches (I prefer that to "AI") for enhancing super-resolution microscopy by @orangeroad2017.bsky.social, Yang Zhang and colleagues in @natmethods.nature.com: doi.org/10.1038/s415...
Mogwai
Fuck it I don’t care anymore
Wow, this sounds like an incredible opportunity!
I’ve already highlighted this landmark #lipidtime paper by @nadlerlab.bsky.social & colleagues, but ICYMI, do read André’s thread — this study is a huge leap forward in understanding the logic of intracellular lipid flux & is a phenomenal example of #chembio probes 🤝 quantitative imaging 🤝 modeling!
A bit delayed, but excited to still share our latest paper, showing that intercellular forces transduced by E-cadherin activate EGFR-ERK signaling in epithelia by inducing EGFR ligand shedding! Mechanical and biochemical signals can act together within a single, linear cascade! tinyurl.com/mr9mj9j2
🍀🔬
MSL10 is a high-sensitivity mechanosensor in the tactile sense of the Venus flytrap @natcomms.nature.com from Toyota lab.
www.nature.com/articles/s41...
What i meant is, can you utilize anything for post correction on already made movies?
Cell migration is a key cellular process that drives major developmental programs and diseases.
Different assays have been developed, but they are often used interchangeably.
In our new paper, we describe how to select the optimal assay.
More details here: www.nature.com/articles/s41...
