Zach Marin

We have two funded postdoctoral positions available. Topics encompass:

-Next gen light-sheet fluorescence microscopy instrumentation

-Structured illumination microscopy and other approaches to extend the resolution limit.

-Nonlinear microscopy combined with adaptive optics / phase conjugation

I'm recruiting 1-2 grad students through the AITHYRA-CeMM PhD program! Applications are due January 30th. This is a fully-funded PhD program, combining AI and biology to advance biological discovery. Please forward to anyone who may be interested! You can apply here: apply.cemm.at

Whiteboard with a drawing of several bears. One bear is thinking, “where am I? I feel so lost down here.”

Some new art popped up in our microscope basement. Big fan

Direct labeling of microtubule turnover reveals in-lattice repair and stabilization patterns in developing neurons The microtubule cytoskeleton is the backbone of neuronal morphogenesis, driving the development of the dendrites and axon, and supporting trafficking to distant compartments. How neuronal microtubules...

🚨The Neurocyto lab is branching out in our latest preprint! We used tubulin microinjection to directly visualize microtubule turnover in developing hippocampal neurons, demonstrating the presence of in-lattice repair and a selective stabilization in the nascent axon. Check below, or read on 🧵 1/9

Dear Sir Paul, Re: Royal Society Code of Conduct I am sure that many scientists have written to you about the specific question of Elon Musk’s Fellowship and whether, under the Royal Society’s Code of Conduct, his retaining that Fellowship is appropriate. I will not rehash these issues. Instead, as a female scientist with extensive experience of activities aiming to increase equality, diversity and inclusion in the engineering and physical sciences sector, I am writing to you (in a personal capacity) to ask you to reconsider the statements you have recently made in this context to the UK press about the Royal Society’s Code of Conduct and how it is applied. A 2018 report from the joint National Academies of the United States of America, concluded that “sexual harassment is common in academic science, engineering, and medicine” and that “greater than 50 percent of women faculty and staff and 20–50 percent of women students encounter or experience sexually harassing conduct in academia”. This report described codes of conduct that make clear that sexual harassment is unethical and will not be tolerated as a “powerful incentive for change”. The authors also noted that sexual harassment can have significant and damaging effects on the integrity of research. In my own praxis, I have found that clear and consistently-implemented codes of conduct that address these issues make female scientists and engineers safer, and allow them to focus more effectively on their research. For codes of conduct to have such a positive effect, it is vital that sanctions for actions which transgress the code are meaningful and substantial.

I was hence aghast to realise that in an interview with the Financial Times published on 9/1/26, you appear to have suggested that the Royal Society “should only expel fellows if their science proved “faulty or fraudulent or highly defective””. Moreover, in a further interview with the Guardian on 11/1/26 you suggested that the code “may need to be looked at again”, with the implication that your aim would be to remove the option of sanctions on Fellows for reasons not strictly related to faults or defects in their research. I suggest that changing the Royal Society’s code of conduct so that the likelihood of serious sanctions for sexual harassment is reduced, would directly endanger women who interact with the Royal Society at events or otherwise, and would provide a licence to harass to the already powerful people on whom the Society bestows fellowship. The implications of your words - that under your leadership the only infringements of the code which are likely to receive the sanction of the Fellowship being removed are those related to research misconduct - already risk empowering harassers. You stated, in the Financial Times interview, that “there’s many bad people around, but they have made scientific advances”. Given this awareness of the possibility of bad actors in our scientific community, it is wholly irresponsible to suggest that the Royal Society would not act to sanction these people if they harass more vulnerable scientists. I am hence writing to request that you retract any suggestion that the Society’s Code of Conduct should be changed so that the only reason a Fellow might be sanctioned by the removal of their Fellowship is “faulty or fraudulent or highly defective” research. This action is necessary to safeguard female scientists, a requirement placed on the Society by safeguarding legislation and UK statutory guidance. Yours sincerely, Professor Rachel A. Oliver.

Following coverage over the weekend of Sir Paul Nurse's comments that suggested that the only reason that a Fellow should be expelled from @royalsociety.org is scientific misconduct, I have written to him to explain the risks such an attitude poses of increasing sexual harassment in STEM.

Manim (www.manim.community) is such a neat tool for generating videos that describe microscopy theory. It’s possible to animate a fluorophore behaving as a Lorentzian with a single line of code—amazing! Code (I’m so sorry about the variable names) here: github.com/zacsimile/ra...

Coffee stains: not just for furniture

It’s an interesting argument: “If you want to remove Musk from the Royal Society, you better be prepared to remove other scientists who have exhibited bad behavior.” I think that sounds fine.

Now out in @natcomms.nature.com: www.nature.com/articles/s41...! The latest GitHub commits/Colab notebooks enable simulation with 3D sequences.

4Pi-SIMFLUX: 4Pi single-molecule localization microscopy with structured illumination - Nature Methods 4Pi-SIMFLUX is a single-molecule localization microscopy approach that achieves a near-isotropic resolution below 10 nm in whole mammalian cells.

We are happy to share our latest work, 4Pi-SIMFLUX, which combines structured illumination with interferometric detection to achieve near-isotropic 3D localization precision of 2–3 nm and resolve sub-10 nm structural features across whole mammalian cells.
www.nature.com/articles/s41...
rdcu.be/eQVxt

A correlative quantitative phase contrast and fluorescence super-resolution microscope for imaging molecules in their cellular context Fluorescence microscopy has been widely used to reveal the spatial distribution of specifically labeled molecules, but it is blind to cellular context. Quantitative phase contrast microscopy (QPC) pro...

Super-resolution single-molecule fluorescence combined with quantitative phase contrast. This powerful combo enables ~0.05 nm optical path difference detection, < 20 nm resolution, and continuous live-cell imaging with digital staining
doi.org/10.1101/2025...
#Microscopy #CellBiology #OI-DIC #SMLM

We present multi-immersion Oblique Plane microscope (miOPM), a light-sheet platform that can be adapted to a wide range of applications, from sensitive live cell imaging to imaging organs and cleared tissues.
www.biorxiv.org/content/10.1...

Localization of single molecules with structured illumination and structured detection - Light: Science & Applications Light: Science & Applications - Localization of single molecules with structured illumination and structured detection

Happy to share this article with my views on @elislenders.bsky.social and @vicidominilab.bsky.social work and discussing current developments in single-molecule localization combining structured excitation and detection. So many exciting perspectives in the field!

www.nature.com/articles/s41...

Highly efficient 12-color multiplexing with speed-optimized DNA-PAINT. We are excited to share our latest paper in @natcomms.nature.com, using left-handed DNA to extend speed-optimized DNA-PAINT to 12 targets in a simple and straightforward way! 🧬👈🚀https://www.nature.com/articles/s41467-025-64228-x

Sketches of six stages of cytokinetic development of the intercellular bridge are illustrated with exmaple U-ExM fluorescence microscopy images. Septin2-GFP shown in green. Tubulin shown in magenta. A shortened workflow illustrates the image alignment and averaging process to generate average 2D reconstructions of cytokinetic stages.

It is out! 🦚 I recorded hundreds of #ExM 🔬images of cytokinetic bridges and averaged them into 6 stages. How? With help from our fantastic collaborators @zacsimile.bsky.social and @jonasries.bsky.social in Vienna 😇. Check out the full atlas here: doi.org/10.5281/zenodo.17232370

Now out on bioRxiv. 🥳My research on #cytokinesis, averaging thousands of #ExM images🔬, creating a dynamic atlas of cytokinesis 🦠⏳. Here's an animated sneak peek of what we found. Better resolution on bioRxiv😄 #PSFoftheGIF

Image quality metrics fail to accurately represent biological information in fluorescence microscopy Image processing methods offer the potential to improve the quality of fluorescence microscopy data, allowing for image acquisition at lower, less phototoxic illumination doses. The training and evalu...

Hello! Very excited to share our latest preprint, which is great news for us but terrible news for any diehard fans of PSNR and SSIM as image quality metrics in microscopy... (1/5)
www.biorxiv.org/content/10.1...

Automated optogenetic control of hundreds of cells in parallel. Each cell is individually steered, collectively acting as a "tissue printer". Preprint & code out! www.biorxiv.org/content/10.1...

Scalable and lightweight deep learning for efficient high accuracy single-molecule localization microscopy Nature Communications - This study presents LiteLoc, a lightweight and scalable AI model for efficient and accurate single molecule localization microscopy data analysis, bringing real-time...

We’re excited to share LiteLoc — a lightweight and scalable deep learning framework for high-throughput single-molecule localization microscopy, enabling analysis speed of >500 MB/s on 8× RTX 4090 GPUs without compromising accuracy. rdcu.be/eztp6

🚨 2 × PhD positions @EPFL! 🚨
Help us push the boundaries of fluorescence microscopy - DNA nanotech, custom optics & spatial omics in Lausanne 🇨🇭. Start Jan 2026. Send CV + motivation + 2 refs → fschueder@ethz.ch
#PhD #Hiring #microscopy #SuperResolution #SpatialOmics #DNAPAINT #FLASHPAINT

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There was a vaccine for Lyme disease, but production was canceled due to insufficient demand. www.cdc.gov/lyme/about/l...

Scientists hide messages in papers to game AI peer review Some studies containing instructions in white text or small font — visible only to machines — will be withdrawn from preprint servers.

Human scientists anticipate human reviewers will use machines, so they put tiny white text to prompt machines to give positive reviews. I’m not even angry, I’m impressed www.nature.com/articles/d41... Scientists hide messages in papers to game AI peer review

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A picture of an ice maker full of ice cubes

Good news I've fixed the worst thing about Europe

schematic illustration of protein labeling using the spontaneous self-complementing peptide protein split-HaloTag system. POI: protein of interest

Pairwise combination of Hpep11 (TOM20-tagged) with the other three Hpep variants 8, 9 and 10 (H2B-tagged) for FLIM multiplexing. The total fluorescence intensity composite, the two separated species and their corresponding wavelet-filtered phasor plot used for species separation are presented.

Live-cell confocal imaging of histone H2B type-2E-Hpep11 CRISPR KI cell lines after 2-hours labeling with the specified CA- ligand [100 nM]. Images were taken with optimal image acquisition parameter for each dye. Scale bar: 50 μm.

(a) Confocal laser scanning microscopy (CLSM) and STED images of mitochondria in U2OS cells coexpressing cpHaloΔ3 and TOM20-Hpep, either overexpressed or endogenously tagged. Scale bar: 1 μm. Pixel intensities scaled according to reference bar. (b) Representative CLSM, STED images of the CRISPR/Cas9 KI cells expressing TOM20 tagged with intact HaloTag (upper) or Hpep11 (bottom). (c) Intensity profiles along mitochondrial tubules (red and blue lines in b). Scale bar: 2 μm. (d) Representative CLSM and STED images of endogenous Hpep11-tagged clathrin with cpHaloΔ3 coexpression. Scale bar: 10 μm (overview) and 2 μm (magnification). (e) Representative CLSM, STED images of endogenously tagged tubulin beta 4B with Hpep11. Scale bar: 10 μm (overview) and 2 μm (magnification). (f) Intensity profiles along tubulin filaments (red and blue lines in e) Means ± s.d. of the filament diameters were calculated as full width at half maximum (FWHM) from n=20 microtubule filaments, ≥ 2 images. A slight increase in cytosolic signal was noted in cells tagged with split-HaloTagat TUBB4B, compared to cells tagged with the full-length HaloTag, which may result from the presence of unbound but labeled cpHaloΔ3. All images were acquired after labeling with CA-SiR [100 nM] for one hour.

New preprint by @kjohnsson.bsky.social lab!

A new split Halotag system with higher affinity of the complements + lower background. The system works with our SiR-CA & CPY-CA halotag ligands and enables STED imaging or FLIM multiplexing.

The short 14 aa tag Hpep enables easy cloning free CRISPR-KI.

🚨🔬💗Whether investigating cell organelles or mapping proteins, together with Victor Puelles's lab we lay a roadmap for selecting optimal #ExM and #SuperResolution #microscopy combinations. Daria Aristova and Dominik Kylies review with amazing co-authors

pubs.aip.org/aip/apr/arti...

Tiny yellow bird waiting at the metro stop this morning

Sidelobe-free deterministic 3D nanoscopy with λ/33 axial resolution - Light: Science & Applications A purely physical, single objective-lens strategy (UNEx-4Pi) for achieving sidelobe-free λ/33 axial resolution by fusion of ultrahighly nonlinear excitation of photon avalanches and mirror-assisted bi...

New work from Qiuqiang Zhan. Nonlinear multiphoton excitation eliminates side lobes in 4Pi, achieves 26 nm axial resolution: www.nature.com/articles/s41...

Your yearly reminder to acknowledge the core facilities you use and their staff scientists in your papers. These scientists are a crucial part of the scientific ecosystem and to continue to exist they need tangible credit for their work. Plus their associated expertise adds credibility to your work.

Thanks! Yep, we do 3D excitation (z scan with a top hat) and 3D modeling of fluorophore positions. See, e.g., example2.