Loading video...

Video Failed to Load

Go Home

From 3D imaging to therapy Using our DISCO tissue clearing and whole organ 3D imaging platform, we revealed skull to meninges microchannels connecting calvarial bone marrow with the brain borders in mice (Cai...Ertürk, Nature Neuroscience,2018, We then extended this biology to humans, discovering distinct skull bone marrow programs and...

15,901 views • 6 months ago •via X (Twitter)

0 Comments

No comments available

Comments from the original post will appear here

Related Videos

How does an embryo reliably "compute" its form - "cell by cell" - using only local interactions and mechanics, yet produce a precise global body plan? I’m excited to share our Nature Methods paper "MultiCell: geometric learning in multicellular development", presenting #AIxBiology research led by Haiqian Yang and the result of a great collaboration with Ming Guo, George Roy, Tomer Stern, Anh Nguyen and Dapeng Bi. A long-standing challenge in developmental biology is to predict how thousands of cells collectively self-organize as tissues fold, divide, and rearrange. In MultiCell, we represent a developing embryo as a dual graph that unifies two complementary views of tissue mechanics with single-cell resolution: cells as moving points (granular) and cells as a connected foam (junction network). This lets the model learn dynamics from both geometry and cell–cell connectivity. On whole-embryo 4D light-sheet movies of Drosophila gastrulation (~5,000 cells), our model predicts key cell behaviors and the timing of events, including junction loss, rearrangements, and divisions with high accuracy, at single-cell resolution. Beyond prediction, the same representation supports robust time alignment across embryos and offers interpretable activation maps that highlight the morphogenetic "drivers" of development. The broader goal is a foundation for cell-by-cell forecasting in more complex tissues, and eventually for detecting subtle dynamical signatures of disease. Kudos to the team for this inspiring collaboration with brilliant researchers to push the boundary of AI for biology! Citation: Yang, H., Roy, G., Nguyen, A.Q., Buehler, M.J., et al. MultiCell: geometric learning in multicellular development. Nature Methods (2025), DOI: 10.1038/s41592-025-02983-x Code/data links are in the manuscript.

Markus J. Buehler

387,977 views • 7 months ago

⚡️📣👇Tremendously excited to share our new Cell article, where we develop TriPath, a method for analyzing 3D pathology samples using weakly supervised AI. Article: TriPath enables 3D computational pathology via 3D multiple instance learning allowing AI models to capture intricate morphological details from pathology volumes. Code: Blog post: Tested on two different imaging modalities, and patient cohorts from two institutions. Our superstar Andrew H. Song put in a monumental effort of leading the study, in a fantastic collaboration with Jonathan Liu at University of Washington . Interesting aspects: - Utilizing the whole tissue volume and leveraging 3D deep learning enable superior risk prediction performance compared to 2D deep learning baselines based on a few sampled tissue sections that emulate standard clinical practice. This indicates TriPath can harness additional information provided by 3D tissue morphology. - The performance is also superior to clinical baselines from a reader study that involved six expert pathologists. - The morphologically heterogeneous tissue volume could lead to opposing patient-level outcome predictions, dependent on which portion of the tissue volume is used. This concurs with current clinical literature warning that tissue sampling bias can lead to misdiagnosis. Some limitations: - While the 3D pathology cohort size is unprecedented, it is smaller than typical 2D pathology cohorts. Further large-scale studies will be required for validation. Nevertheless, we believe that this study will initiate a positive cycle, encouraging academic institutions and pharmaceutical companies to contribute large banks of human tissue blocks with paired clinical outcomes, thus speeding up advancements in 3D computational pathology. Concluding insights: We believe that 3D pathology is just around the corner - It has the huge potential to not only augment/improve the current clinical practice centered around 2D examination of human tissue, but also help reveal novel biomarkers for prognosis and therapeutic response.. Harvard Medical School Harvard Data Science Initiative Mass General Brigham Broad Institute

Faisal Mahmood

65,541 views • 2 years ago

Science Corner: David Friedberg Explains Recent Mitotherapy Breakthroughs ⚡️ On E224, david friedberg broke down what mitotherapy is and how recent discoveries could unleash this treatment for many diseases: "So mitochondria are the powerhouse of the cell." "Every cell in our body gets its energy, which is what it uses to function, from the mitochondria." "And so there's been a lot of research into the relationship between mitochondria and aging, and that dysfunctional mitochondria may actually be a key driver for many diseases." "Including many cancers, Alzheimer's, Parkinson's, ALS, features of autism, muscle tissues being weak, etc." " So, as the cells get older and the mitochondria stop working, we make new mitochondria." "But over time, the DNA degrades and the mitochondria become less effective and there are fewer functional mitochondria per cell." Friedberg highlighted three recent papers: 1) "The power and potential of mitochondria transfer" (nature) -- "these folks identified and demonstrated that mitochondria can actually transfer from one cell to another" -- " So, if you've got a cell that's got damaged, or dysfunctional mitochondria, they've identified three mechanisms by which mitochondria can move into a cell that needs more mitochondria that are working and are more functional." -- "And as a result, it can rejuvenate or provide energy to a dysfunctional cell, which might improve dysfunctional tissue or improve disease." 2) "A human brain map of mitochondrial respiratory capacity and diversity" (nature) -- " this was the first mapping of the mitochondria in the human brain" -- " what it showed was that different parts of the brain, different cells, had different amounts of mitochondria and different mitochondrial function." -- "(This) starts to highlight how that difference in energy production in different cells in different parts of the brain may actually cause some of the things like memory loss or speech impairment," -- "the mitochondrial dysfunction in the brain might actually be the key driver of that aging symptomology." 3) "Organelle-tuning condition robustly fabricates energetic mitochondria for cartilage regeneration" (nature | Bone Research) -- " (the researchers) figured out a way to treat stem cells so that (they) would start to make an excess amount of mitochondria than they normally would make" -- " So they created highly energetic mitochondria and they made a lot of them." -- " the idea that we can put mitochondria into our body or into tissue in our body to heal it or repair it has been something that folks have been trying to do research around for a long time" -- " but the limiting factor is access to enough mitochondria" -- " so this mechanism that they developed opens up the door to this whole new therapeutic modality, a new type of therapy called mitotherapy" Conclusion: " ... based on the series of papers that we're seeing coming out recently, I believe (this) could end up becoming a really incredible new therapy that may ultimately lead to the treatment for many diseases that we're dealing with right now."

The All-In Podcast

58,412 views • 1 year ago

Single-cell technologies now let us profile entire transcriptomes in individual cells. But how do we make sense of this complexity in a biologically meaningful way? Many methods summarise cells into a single embedding, but this often comes at the cost of interpretability, especially when multiple gene programs are active at once. We developed Tripso, a self-supervised transformer model that represents cells through multiple gene program-specific embeddings, while also uncovering new programs directly from the data. Instead of collapsing biology into a single vector, Tripso decomposes cell state into multiple representations, each reflecting a different gene program. We explored this across multiple systems. In human hematopoiesis, spanning development to aging, Tripso identified distinct age-associated program activity, including stronger JAK-STAT signalling in early life and dynamic IKZF1-related changes during B cell maturation. By comparing in vitro culture conditions with in vivo hematopoietic stem cell states, Tripso suggested that targeting the SEC61 translocon could enhance stem cell maintenance ex vivo, a prediction that we subsequently validated experimentally. In parallel, we identified a previously uncharacterised tissue-resident memory T-cell program associated with atopic dermatitis and mapped it to distinct spatial immune niches Together, these results show how modelling cells through gene programs can lead to interpretable and experimentally testable insights. More broadly, this work points toward a more interpretable and biologically grounded models of cell state. As single-cell datasets continue to grow, we hope approaches like Tripso will help bridge the gap between data-driven representations and biological insight. This work wouldn’t have been possible without the contributions of an amazing team. Thank you to co-first authors Marie, Tomoya Isobe, Amirhosein Vahidi, Carlo Leonardi, and everyone from roser's Lab, Haniffa Lab, Nicola Wilson and Bertie Gottgens's Lab, bringing together expertise across Cambridge Stem Cell Institute, Open Targets, Wellcome Sanger Institute and Cambridge University. Marie is one of the very best PhD students I have ever supervised. She is truly a force of nature, exceptionally resourceful, deeply innovative, and one of the most impressive scientists I have worked with. I am immensely proud of her and all that she has accomplished. As she begins her internship at Genentech , I have no doubt she will do amazing work there and continue to make her mark. paper: code:

Mo Lotfollahi

22,464 views • 4 months ago

Excited to share our new work on building a multimodal atlas of human skin in health and inflammatory disease — a project I’m especially proud of, bringing together AI, high-throughput genomics, and clinical science to accelerate discovery. Over the past decade, single-cell genomics has transformed how we map cells in human tissues. But a major challenge remains: can we systematically decode how cells organize into functional niches in situ — including those invisible to standard histopathology? To address this, we integrated large-scale scRNA-seq, spatial transcriptomics, histopathology, and AI-driven modeling frameworks to build an in situ atlas of human skin across health and disease. Led by Lloyd Steele, an MD/PhD student working between Haniffa Lab and my lab at Wellcome Sanger Institute and Cambridge University . Another amazing collaboration with Muzz Haniffa, the mastermind behind the work as part of Human Cell Atlas. A key part of this study is that we didn’t build everything from scratch — we leveraged and combined AI methods that actually work! and showed how they can be used together to extract biological insight at scale. We used: • scArches to build and map into a reference scRNA-seq atlas of human skin: • NicheCompass to identify and characterize spatial niches: • MINT-Flow to extract microenvironment-induced cell states and gene programs: Together, these enabled an end-to-end workflow from atlas construction to spatial mapping, niche discovery, and cell state decoding. At scale, we integrated ~5 million cells and 100+ spatial sections, enabling a systematic view of tissue organization. Using this framework, we identified 26 niches in skin, including known histopathologic structures as well as hidden disease-associated niches not visible on H&E. Among the most striking findings were a resident memory T cell-rich sebaceous gland niche and a plasma cell-rich sweat gland niche, suggesting that appendageal structures act as active immunological microenvironments and may contribute to inflammatory memory and disease persistence. Importantly, this atlas is not just descriptive — it is usable. It can support mapping of new datasets, resolve finer cell types and niches, extract microenvironment-driven programs, and enable predictive analyses at scale. More broadly, this work shows what becomes possible when AI, spatial genomics, and atlas-scale data are integrated end-to-end: not just mapping tissues, but systematically decoding them. This was a massive collaboration, and I’m very grateful to the amazing scientists April Foster, Kenny Roberts, and Chloe Admane. Lloyd is an amazing scientist, and I’m especially excited for the community to see more of his work soon — stay tuned. The data and pre-trained models will be released soon. Preprint:

Mo Lotfollahi

11,802 views • 4 months ago

A new Nature paper from Johns Hopkins (by Prof. Lin Dingchang Lin ) just solved one of the hardest problems in biology: how do you record what every cell in a tissue experienced over time, not just what it looks like right now? The answer: GEMINI — Granularly Expanding Memory for Intracellular Narrative Integration. It works exactly like tree rings. Cells are genetically engineered to express a computationally designed protein assembly. As the assembly grows inside the cell, it captures cellular activity as fluorescent ring patterns — each ring a timestamp, each ring's properties encoding signal intensity. Look at a cross-section under a microscope and you can read the cell's history backward, with ~15-minute resolution. The key: cells build the recorder themselves. GEMINI doesn't interfere with normal function — it just quietly writes. What they demonstrated: In a full tumor xenograft, GEMINI captured every cancer cell's activity history across the entire tumor while it continued to grow normally. For the first time, researchers can look back and see how different regions of the same tumor responded differently to therapy over time — not snapshots, but film. In a mouse brain, GEMINI recorded neural activity dynamics without disrupting behavior, coordination, or memory. It could temporally resolve the history of a brain seizure. Why this matters: Every tool we have in biology gives you state — what the cell looks like now. Sequencing, imaging, proteomics — all snapshots. GEMINI gives you trajectory. It's the difference between a photograph and a video, applied to every cell in an organ simultaneously. The team is explicit that AI-based decoding tools will be central to reading GEMINI's output at whole-brain scale. This is the data layer that makes temporal single-cell atlases possible. Paper: Congratulations Dingchang Lin

Bo Wang

85,146 views • 5 months ago

"The real dangerous thing about the Pfizer DNA". "It's like one of these self-amplifying RNA's". Genomics expert Kevin McKernan has seen DNA contamination 10- to 100-fold above safety limits and they haven't even tested the "E Lots" containing the super dangerous vials. "[In] a study from Professor Ulrike Kämmerer in Germany [she] transfected cell lines with the vaccine in petri dishes [and] she watched those through several cell divisions, and the SV40 was staying with them throughout the cell divisions." Transcript, Kevin McKernan: "That's the really dangerous thing about the Pfizer DNA. Unlike the Moderna DNA, they left a mammalian origin of replication in there. So, if it gets into a mammalian cell, it's capable of making more copies of itself once it's in there. In essence, it's like one of these self-amplifying RNAs that everyone's ludicrously thinking about releasing right now. There has been a study from Professor Ulrike Kämmerer in Germany where she transfected cell lines with the vaccine in petri dishes. Not the virus—I'm sorry, the vaccine. I might as well call it a virus at this stage, and she watched those through several cell divisions, and the SV40 was staying with them throughout the cell divisions. That's a sign that it is replication-competent to some degree. That's still yet to be done with the really egregious lots—the E lots. I bet if we did those, there would be full-length plasmids in those, and they would stay permanently in those cell lines. But we don't have access to those. For those not familiar with these E lots, there's a Schmeling et al. paper that showed that about four percent of the lots are responsible for about 77% of the adverse events. None of those have been surveyed yet for this. We're finding contamination 10- to 100-fold above the limit in the lots that had low adverse events. Wait until we get to the ones that are really hurting people."

Humanspective

15,938 views • 1 year ago

We’re thrilled to share that our MERFISH+ preprint is now live on bioRxiv!👉 In this work, the Bintu and Zhu labs (UCSD) developed MERFISH+, a next-generation spatial genomics platform that combines genome-wide RNA and epigenetic imaging over a large field of view. By introducing acrydite-modified probes covalently anchored to hydrogels, MERFISH+ achieves remarkable imaging stability and enables >1,800-gene, multi-modal, and multi-month experiments. With this platform, they, together with the Chi lab at UCSD, profiled a whole developing human heart at 12 post-conception week with merely two slides, resulting in a total of 53 slides, 3.1 million single cells and more than 30 cell types. Building upon our previous 3D reconstruction and modeling framework, Spateo ( we reconstruct the 3D human heart that nicely captures the anatomical structure of the heart, including the intricate vasculature network. Sophisticated analyses provide a holistic view of an entire organ and enable systematic characterization of 3D cellular neighborhoods and transcriptional gradients of substructures such as the descending arteries. Furthermore, using a generative integration framework for spatial multimodal data (Spateo-VI), we harmonized these MERFISH+ transcriptomic and chromatin data to reconstruct a 3D spatially-resolved multi-omics atlas of the developing human heart, shared at and MERFISH+ thus sets a new standard for large-format, multi-omic spatial profiling, enabling holistic, 3D characterization of organs at subcellular resolution. Huge congratulations to first authors Colin Kern, qingquan Zhang, Yifan Lu , and Jacqueline Eschbach, and to all collaborators from the Bintu, Zhu, Chi, and Qiu labs for this amazing team effort. Thanks for your diligence, creativity, and hard work on this project. We’re grateful for support from Arc Institute and our generous donors. Our lab is expanding—if you’re excited about building the next generation of single-cell and spatial genomics techniques and predictive single cell and spatial foundation models, we’re hiring! If you are interested, please reach out to me via direct message or email at [email protected]. We are excited for any potential collaborations along this line of research in Stanford, UCSF and Berkeley and other labs as well.

evo-devo

42,208 views • 9 months ago

🚀 We’re hiring! Staff Scientist / Postdoc – Tissue Clearing & 3D Image Analysis (m/f/d) (LMU Munich) Are you a great fit, or do you know someone outstanding, please reach out 🔁 If you want to at the frontier of whole-organ / whole-body 3D imaging, and help generate truly beautiful datasets that drive major biological discoveries and therapeutic development, see below ✨ We’re building the next-generation pipeline for tissue clearing + light-sheet microscopy + quantitative 3D analysis in the SyNergy Excellence Cluster (Mesoscale Hub) and we’re looking for someone excited to push this forward with us. 🧠🔬📈 🎥 I’m also attaching a short video showing the kind of high-quality imaging and datasets you’d be working with. What you’ll do 🛠️ 🔹 Lead and evolve tissue clearing + light-sheet workflows across collaborative SyNergy projects 🔹 Turn complex 3D datasets into robust quantitative insights (visualization, atlas registration, readouts) 🔹 Develop new methods and analysis pipelines together with our AI team 🤖 🔹 Maintain and optimize cutting-edge light-sheet systems (optional: support animal license writing) What we’re looking for 🎯 ✅ Strong hands-on experience in tissue clearing and/or fluorescence microscopy ✅ Solid experience with light-sheet microscopy and 3D imaging workflows ✅ Familiarity with 3D tools like Imaris / arivis Vision4D, stitching (e.g., BigStitcher), and quantitative analysis in cleared tissues ✅ Service mindset, great organization, and strong scientific English How to apply 📩 Apply via the LMU Klinikum online application form Please also send your application to: [email protected] CC: [email protected] 📎 Include one PDF: short cover letter, CV, 2–3 referees, and earliest start date. 📍 Campus Großhadern (Munich) and Helmholtz Munich | 🕒 Full-time | 📅 Start: 01 January 2026 If you love high-quality imaging, cutting-edge biology, and building something that will matter, we’d love to hear from you. 🌍✨ #hiring #StaffScientist #Postdoc #TissueClearing #LightSheetMicroscopy #ImageAnalysis #SpatialBiology #Neuroscience #SyNergy #LMU #Munich

Ali Max Erturk

14,751 views • 7 months ago

When I caught Covid, my friends rushed doses of Ivermectin to me — kicked Covid in 24 hours. Here’s a cancer surgeon revealing her discoveries about the impact of Ivermectin on CANCER… 9 min. must see: Also — Compelling Evidence for Ivermectin in Treating Covid: · Front Line COVID-19 Critical Care Alliance Review — This review, which summarized findings from 27 studies, concluded that ivermectin demonstrates a strong signal of therapeutic efficacy against COVID-19. This includes both prevention and treatment aspects. · Meta-Analysis on Ivermectin — A meta-analysis covering 96 studies and over 135,000 patients suggests that ivermectin has shown effectiveness in combating COVID-19. This analysis points towards ivermectin's role in reducing severity and improving health outcomes. · Antiviral Effect Study — A study aimed at assessing the antiviral effect of high-dose ivermectin found it to have an impact on viral load, suggesting its potential in reducing the severity of the disease by decreasing the viral replication. Evidence for Ivermectin in Treating Cancer as summarized by Dr. William Makis, Radiologist, Oncologist, Cancer Researcher. NEW ARTICLE: IVERMECTIN and Protocols for CANCER Ivermectin has a dozen anti-cancer mechanisms but they can be summarized into two main ones: 1. Inhibits cancer proliferation signaling pathways (Akt, mTOR, Wnt) 2. Inhibits Cancer Stem Cells IVERMECTIN will act against regular CANCER as well as Pfizer and Moderna COVID-19 mRNA Vaccine Induced TURBO CANCER (which is highly resistant to chemo) Here are recent studies on IVERMECTIN use in certain types of cancer: BLADDER CANCER - (2024 Fan et al) - Ivermectin Inhibits Bladder Cancer Cell Growth and Induces Oxidative Stress and DNA Damage LUNG CANCER - (2024 Man-Yuan Li et al) - Ivermectin induces nonprotective autophagy by downregulating PAK1 and apoptosis in lung adenocarcinoma cells GLIOMA - (2024 Xing Hu et al) - Ivermectin as a potential therapeutic strategy for glioma MULTIPLE MYELOMA - (2024 Yang Song et al) - Gene signatures to therapeutics: Assessing the potential of ivermectin against t(4;14) multiple myeloma OVARIAN CANCER - (2023 Jawad et al) - Ivermectin augments the anti-cancer activity of pitavastatin in ovarian cancer cells PROSTATE CANCER - (2022 Lu et al) - Integrated analysis reveals FOXA1 and Ku70/Ku80 as targets of ivermectin in prostate cancer COLON CANCER - (2022, Alghamdi et al) - Efficacy of ivermectin against colon cancer induced by dimethylhydrazine in male wistar rats PANCREATIC CANCER - (2022 Lee et al) - Ivermectin and gemcitabine combination treatment induces apoptosis of pancreatic cancer cells via mitochondrial dysfunction MELANOMA - (2022 Zhang et al) - Drug repurposing of ivermectin abrogates neutrophil extracellular traps and prevents melanoma metastasis IVERMECTIN has proven anti-cancer activity against some 20 cancer types, although these are pre-clinical studies. We will never see clinical studies because Ivermectin is off patent and cheap. Merck, which used to have a patent on Ivermectin, has partnered with Moderna on mRNA Cancer Vaccines. IVERMECTIN is so safe, that in much of the civilized world, it is available over the counter, no prescription needed. Ivermectin is annually taken by close to 250 million people.

Bobby

160,026 views • 1 year ago

🚨🚨🚨 Dutch Cancer Researcher and Erasmus Medical Centre Assc Prof Maarten Fornerod discusses DNA contamination in COVID Vaccines. ---------------------------- ...for last 35 years or so I've been working uh in the areas of molecular biology, gene expression, biology, cancer biology and recently in the last years, maybe last 10 years in the context of big data and computational biology... ...when we use genetic vaccines what we do essentially is we're making a complex intervention in a very complex system. It's impossible to predict what happens if you combine these two complex systems, and you get unpredictable effects. .. And the only way to go about this is to do genotoxic research, when you want to introduce a genetic medicine into a human being and that genetotic research has to be independent, it has to be double blind, has to be long lasting. AND ALL THESE HAVE NOT BEEN DONE WITH THE GENETIC CORONA VACCINES! if there's a vaccine, there's a little bit of DNA in there upon injection that is very, very rapidly degraded by the human body. However if it's protected and in a lipid nanoarticle it can very efficiently be transduced in the cell... I've been doing this this many, many times. This is called lipofection and it's a very efficient way to introduce DNA into a cell. ...Many people think that this is not possible. But I've been working in nuclear transport for many years, I think more than 10 years. So I've been exposed to a lot of molecular cell biology of nuclear cytoplasmic transport. And it's clear that the DNA can enter the nucleus. Now to make things worse, the mRNA vaccine doesn't stay in the arm but it's detected in , in all different organs including the reproductive system. And so partly this is based on animal models, of course we know from Michael Morz that he has detected uh the spike protein in brain, in the heart and it's for sure it's detected in the blood and even in breast milk. ..So there's NO DOUBT that this mRNA vaccine spreads widely in the human body. ..Now from a genetic point of view, there are possible consequences uh of this and the consequences could be a 1. long term disruption of cellular processes that could lead to disease. 2. there's a risk of insertional mutageenesis in somatic cells that can lead to cancer. 3. the insertion mutogenesis takes place in a germ cell which would be a hereditary burden uh on the human population. 4. And you could also think that these um DNAs, could transfect the microbiome and it could possibly lead to bacterial resistance. So these are all possible..the consequences of these genetic vaccines in my view, the shortcomings in this rollout of these vaccines were there was no genotoxic research performed at all. There was no safety studies, on carcinogenic potential of these vaccines. My personal opinion is that it's now not a question of whether, it will integrate in recipient's DNA, but how often it occurs... It's just a numbers game. If you do this in many cells, many persons it will no doubt integrate in cells in human recipients. So the question does it affect the human genome? I would say it probably, I think it most certainly does. And you see Kevin McKernan here and he represented ah a preliminary data where he detected a possible Pfizer DNA in colon cancer biopsy one year after vaccination.

aussie17

126,273 views • 1 year ago