iiinova — where your digital self keeps evolving

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Danielle Beckman @daniellebeckman.bsky.social · 30/07/2026

What if acute COVID seems gone, but parts of the virus aren’t? Our lab is using advanced imaging to see what conventional methods miss, and turn those discoveries into urgently needed #LongCOVID treatments. 🔬 The evidence 👇🏻

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Markus Elsner @markuselsner.bsky.social · 30/07/2026

Check out what we have been up to recently, as we are now trying to make a real-world difference in Long COVID and other diseases

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Ali Maximilian Erturk @erturklab.bsky.social · 30/07/2026

SARS-CoV-2 spike protein accumulates & persists in the body for years👇🏻. We develop advanced imaging/AI to cure Long COVID & beyond👇🏻. Join us 🤗 www.nature.com/articles/s41... www.cell.com/cell-host-mi... www.biorxiv.org/content/10.6... www.biorxiv.org/content/10.6... www.biorxiv.org/content/10.1...

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Ali Maximilian Erturk @erturklab.bsky.social · 28/07/2026

Brain vascular aging isn’t a single path. Our new work shows that the aging brain diverges into two states: 🧠 Hypovascular (expected) 🧠 Hypervascular (surprising), with BBB leakage, inflammation and cognitive decline. Our study👇🏻: www.biorxiv.org/content/10.6...

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Ali Maximilian Erturk @erturklab.bsky.social · 13/06/2026

See our science at Deep Piction, how we use it to develop new precision medicine.

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Hao Yin @haoyin.bsky.social · 05/06/2026

MouseMapper An imaging-omics workflow of whole-mouse analysis Up to single-cell resolution!👹 vDISCO WildDISCO whole-mouse optical clearing #SpatialProteomics Trigeminal ganglia VR annotation of major organs, peripheral nerve & Mφ @erturklab.bsky.social Nature 2026 www.nature.com/articles/s41...

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Markus Elsner @markuselsner.bsky.social · 28/05/2026

Ohhh, wow!

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Ali Maximilian Erturk @erturklab.bsky.social · 28/05/2026

Our recent work in @Nature, MouseMapper uses foundation-model AI, mapping perturbations in mouse body cell-by-cell, revealed unexpected facial nerve damage. Proud to see >75K accesses & >60 news stories in the first week. Paper->> www.nature.com/articles/s41... Next www.biorxiv.org/content/10.6...

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Doris Kaltenecker @dorie00.bsky.social · 25/05/2026

Super happy to see our work published in @nature.com last week 🤩 By combining whole-body tissue clearing, light-sheet microscopy and AI, we mapped obesity-associated remodeling across the entire mouse body in 3D at cellular resolution. www.nature.com/articles/s41... @erturklab.bsky.social

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Ali Maximilian Erturk @erturklab.bsky.social · 20/05/2026

Today in Nature, we report MouseMapper: foundation-model AI to map disease perturbations across the entire mouse body cell-by-cell. In obesity, it revealed body-wide inflammation & unexpected facial nerve damage. www.nature.com/articles/s41... More at: x.com/erturklab/st...

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Waggoner Lab @labwaggoner.bsky.social · 20/05/2026

A deep-learning framework reveals whole-body perturbations at cell level @nature.com @erturklab.bsky.social @dorie00.bsky.social www.nature.com/articles/s41...

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Helmholtz Munich @helmholtzmunich.bsky.social · 20/05/2026

#M1 Launches First Funding Period & Advances Translation in Munich🚀 Seven projects receive €7.45 million through the M1 – Munich Medicine Alliance. #HelmholtzMunich is involved in four funded projects. 👉 t1p.de/disle @tum.de @lmu.de @boyanbonev.bsky.social @erturklab.bsky.social #MunichMedicine

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Helmholtz Munich @helmholtzmunich.bsky.social · 20/05/2026

AI Atlas Reveals Hidden Whole-Body-Damage Caused by Obesity Researchers around Prof. Ali Ertürk, #HelmholtzMunich, developed #MouseMapper – an #AI framework that maps disease-related changes throughout the entire mouse body at cellular resolution. 👉 t1p.de/svfv0 @erturklab.bsky.social

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Markus Elsner @markuselsner.bsky.social · 18/05/2026

I was not very much involved in this project from our lab, but I can honestly say that I find this story really amazing!

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Ali Maximilian Erturk @erturklab.bsky.social · 15/05/2026

🧠 Does brain aging always mean vessel loss? We found the opposite in some aged brains: maladaptive hypervascularization, linked to cognitive decline and blood-brain barrier damage. Check it out below! www.biorxiv.org/content/10.6...

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Ali Maximilian Erturk @erturklab.bsky.social · 13/05/2026

happy to share our new protocol paper on wildDISCO for whole-body immunolabeling, tissue clearing & 3D imaging of intact mice at cellular resolution using standard IgG antibodies, for mapping of neuronal, vascular, lymphatic and immune systems across the entire body. www.nature.com/articles/s41...

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Ali Maximilian Erturk @erturklab.bsky.social · 28/03/2026

𝗬𝗼𝘂𝗿 𝘀𝗰𝗶𝗲𝗻𝗰𝗲 𝗴𝗼𝘁 𝘆𝗼𝘂 𝘁𝗵𝗲 𝗼𝗳𝗳𝗲𝗿. 𝗬𝗼𝘂𝗿 𝗻𝗲𝗴𝗼𝘁𝗶𝗮𝘁𝗶𝗼𝗻 𝘀𝗸𝗶𝗹𝗹𝘀 𝗱𝗲𝘁𝗲𝗿𝗺𝗶𝗻𝗲 𝘄𝗵𝗮𝘁 𝘆𝗼𝘂 𝗯𝘂𝗶𝗹𝗱 𝘄𝗶𝘁𝗵 𝗶𝘁. What would be your negotiation advice to the younger generation?

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Ali Maximilian Erturk @erturklab.bsky.social · 28/03/2026

And to senior PIs and department heads reading this: 𝗵𝗲𝗹𝗽 𝘆𝗼𝘂𝗿 𝘁𝗿𝗮𝗶𝗻𝗲𝗲𝘀 𝘄𝗶𝘁𝗵 𝘁𝗵𝗶𝘀. Share what you know. 𝐸𝑠𝑝𝑒𝑐𝑖𝑎𝑙𝑙𝑦 support the young women in your groups. Every person who negotiates well makes it easier for the next one.

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Ali Maximilian Erturk @erturklab.bsky.social · 28/03/2026

Negotiation isn't a one-time thing. 𝗜𝘁 𝘪𝘴 𝘁𝗵𝗲 𝗷𝗼𝗯. As a PI, we negotiate for grants, contracts, space, and people. How you negotiate your own position signals how you'll fight for your team. Talk to people. Salary transparency in academia is still mostly informal. Build your network and use it.

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Ali Maximilian Erturk @erturklab.bsky.social · 28/03/2026

And importantly: 𝗻𝗲𝗴𝗼𝘁𝗶𝗮𝘁𝗲 𝘣𝘦𝘧𝘰𝘳𝘦 𝘆𝗼𝘂 𝗮𝗰𝗰𝗲𝗽𝘁 𝘁𝗵𝗲 𝗼𝗳𝗳𝗲𝗿. Once you accept, there is usually little to no chance to negotiate later, because your biggest leverage is gone. Take that seriously.

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Ali Maximilian Erturk @erturklab.bsky.social · 28/03/2026

Your leverage is built 𝑙𝑜𝑛𝑔 𝑏𝑒𝑓𝑜𝑟𝑒 the offer arrives. Be great at what you do. Be visible. Generate alternatives. Do your homework on what's possible in terms of salary and start-up packages.

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Ali Maximilian Erturk @erturklab.bsky.social · 28/03/2026

And the data is clear: 𝘄𝗼𝗺𝗲𝗻 𝗱𝗶𝘀𝗽𝗿𝗼𝗽𝗼𝗿𝘁𝗶𝗼𝗻𝗮𝘁𝗲𝗹𝘆 𝗿𝗲𝗰𝗲𝗶𝘃𝗲 𝗹𝗼𝘄𝗲𝗿 𝘀𝗮𝗹𝗮𝗿𝗶𝗲𝘀 and are often expected to stay on the "don't ask" side. That needs to change. A few things I'd tell any junior scientist about to start their first PI or industry position:

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Ali Maximilian Erturk @erturklab.bsky.social · 28/03/2026

Because we don't want to seem "difficult." Here's what I've learned: 𝘁𝗵𝗲𝗿𝗲 𝗶𝘀 𝘢𝘭𝘮𝘰𝘴𝘵 𝘢𝘭𝘸𝘢𝘺𝘴 𝗿𝗼𝗼𝗺 𝘁𝗼 𝗻𝗲𝗴𝗼𝘁𝗶𝗮𝘁𝗲. Even in systems like Germany, where salaries look rigid on paper, top-ups and start-up packages are negotiated all the time. The difference? Some people ask. Others don't.

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Ali Maximilian Erturk @erturklab.bsky.social · 28/03/2026

One thing nobody teaches you in academia: 𝗵𝗼𝘄 𝘁𝗼 𝗻𝗲𝗴𝗼𝘁𝗶𝗮𝘁𝗲. We spend 10+ years learning how to do science, write grants, and present data. But when the job offer finally comes, most people just… accept it. Because we're relieved. Because we think the salary is fixed.

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Ali Maximilian Erturk @erturklab.bsky.social · 18/03/2026

Using vDISCO tissue clearing, and a new ultrabright chemical labeling strategy. This work introduces LINCS for rapid, scalable 3D connectivity mapping from single neurons to whole brains, advances for high-throughput circuit mapping. Great work by Rui Lin lab. www.sciencedirect.com/science/arti...

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Philip Ruthig @philipruthig.bsky.social · 09/03/2026

Be my colleague! :)

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Markus Elsner @markuselsner.bsky.social · 09/03/2026

Come work with us!

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Ruth Ann Crystal @drruth.bsky.social · 09/03/2026

Job available at the amazing Erturk lab in Munich

Photo of blood vessels in the brain in yellow with pink on the periphery and purple at the outer edges.

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Ali Maximilian Erturk @erturklab.bsky.social · 09/03/2026

Hiring in Munich: Staff Scientist / Postdoc in Tissue Clearing and 3D Image Analysis. We’re looking for someone with strong hands-on expertise in tissue clearing, light-sheet microscopy, and quantitative 3D image analysis. Shares and recommendations are very welcome. www.linkedin.com/jobs/view/43...

linkedin.com

LMU Klinikum München hiring Staff Scientist / Postdoc – Tissue Clearing & 3D Image Analysis in Greater Munich Metropolitan Area | LinkedIn

Posted 8:17:54 AM. About us 🧠🔬The Institute for Stroke and Dementia Research (ISD) at LMU Klinikum is a highly…See this and similar jobs on LinkedIn.

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Ali Maximilian Erturk @erturklab.bsky.social · 13/02/2026

In this recent Nature Methods Perspective, I outline how tissue clearing, spatial-omics, and AI converge to create deep 3D histology, enabling unbiased, organism-scale biology and next-generation digital pathology. www.nature.com/articles/s41...

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Ali Maximilian Erturk @erturklab.bsky.social · 08/02/2026

A new preprint introduces aDISCO, a DISCO-based clearing approach that makes whole archival FFPE human tissues transparent and antibody-compatible, enabling true 3D light-sheet histology across brain & multiple organs at cellular resolution. Aguzzi & Helmchen teams. www.biorxiv.org/content/10.1...

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Ali Maximilian Erturk @erturklab.bsky.social · 13/01/2026

We’re hiring – Computer Science PhD at iBIO (Helmholtz Munich / LMU). Build AI-driven, whole-body multi-omics atlases by combining scRNA-seq, spatial transcriptomics, proteomics & 3D imaging. Looking for strong omics data analysis skills with ML/DL. Apply or share: www.linkedin.com/jobs/view/43...

linkedin.com

Helmholtz Munich hiring PhD Position – Deep Learning for Multi-Omics Atlases of the Mammalian Body in Greater Munich Metropolitan Area | LinkedIn

Posted 8:43:27 PM. AI Scientist - PhD Position Institute for Intelligent Biotechnologies (iBIO), Helmholtz Munich /…See this and similar jobs on LinkedIn.

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Markus Elsner @markuselsner.bsky.social · 29/12/2025

This is going to be fun! I promise!

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Ali Maximilian Erturk @erturklab.bsky.social · 29/12/2025

My team at Deep Piction (Munich) is hiring a Senior Director, Drug Discovery (Long Covid) to build and lead our early discovery engine. If you have 10+ years in early-stage biotech/pharma, let’s talk. www.linkedin.com/jobs/view/43...

linkedin.com

Deep Piction hiring Senior Director Drug Discovery in Greater Munich Metropolitan Area | LinkedIn

Posted 10:31:52 AM. Senior Director, Drug Discovery (Long Covid)Location: Munich, Germany (Onsite)Type:…See this and similar jobs on LinkedIn.

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Ali Maximilian Erturk @erturklab.bsky.social · 18/12/2025

Most transcriptomics studies sample ~0.001% of a mouse. Which region do we choose? Often: we guess. Meet DISCO-seq 🤗 flipping the order: RNA-preserving clearing → whole-organ/whole-body 3D imaging → pick ROIs in 3D → unbiased scRNA-seq. Preprint: www.biorxiv.org/content/10.6...

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Markus Elsner @markuselsner.bsky.social · 23/12/2025

Single cell transcriptomics from cleared tissue? Impossible you say? Check out our latest preprint!

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Ali Maximilian Erturk @erturklab.bsky.social · 18/12/2025

✨ DISCO-seq bridges 3D anatomy and single-cell genomics. Unbiased, imaging-guided, whole-organ transcriptomics—from brain tumors to infection biology.

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Ali Maximilian Erturk @erturklab.bsky.social · 18/12/2025

Take-home: most spatial biology still starts from 2D slices + predefined ROIs/genes. DISCO-seq changes the paradigm: whole-organ/whole-body 3D first → unbiased single-cell transcriptomics second.

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Ali Maximilian Erturk @erturklab.bsky.social · 18/12/2025

Spike S1 induces region- and condition-specific gene programs, highlighting spatial immune specialization along the gut.

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Ali Maximilian Erturk @erturklab.bsky.social · 18/12/2025

Small intestine scRNA-seq preserves cell-type diversity across conditions/regions (PBS vs S1; duodenum vs ileum) with expected epithelial, immune, and stromal populations.

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Ali Maximilian Erturk @erturklab.bsky.social · 18/12/2025

Whole-body application: 3D DISCO imaging maps organ-specific SARS-CoV-2 Spike S1 tropism. In the gut, we see distinct enrichment patterns (duodenum vs ileum), enabling unbiased ROI selection.

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Ali Maximilian Erturk @erturklab.bsky.social · 18/12/2025

DISCO-seq resolves region- and cell-type-specific programs in GBM: neurons and microglia show distinct states across core vs remote niches.

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Ali Maximilian Erturk @erturklab.bsky.social · 18/12/2025

Imaging-guided ROI selection enables spatially resolved transcriptomics: tumor core vs remote rostral/caudal ROIs within the intact brain.

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Ali Maximilian Erturk @erturklab.bsky.social · 18/12/2025

3D quantification maps tumor burden across annotated brain regions, distinguishing small blobs, clusters, and large lesions—revealing region-specific heterogeneity

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Ali Maximilian Erturk @erturklab.bsky.social · 18/12/2025

Glioblastoma: whole-brain 3D imaging reveals dissemination beyond the primary lesion. Satellite tumors + contralateral spread become visible in 3D—often missed in 2D or standard clinical imaging.

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