Zach Marin

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

Lyme Disease Vaccine A vaccine for Lyme disease is not currently available, clinical trials of new vaccines are underway.

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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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.

Advancing Super-Resolution Microscopy: Recent Innovations in Commercial Instruments Abstract. Super-resolution microscopy techniques have accelerated scientific progress, enabling researchers to explore cellular structures and dynamics wit

We have a new review out! In this Microscopy & Microanalysis piece, Louisa Mezache and I survey some of the latest commercially available microscope technologies: Nikon NSPARC, Re-scan Gaia, CSR Biotech MI-SIM, refinements to STED, SMLM from Bruker and Abbelight… Check it out with free access:

Check out our new MINFLUX Simulator: www.biorxiv.org/content/10.1... with @zacsimile.bsky.social. Realistic simulation of optics, mechanics, fluorophore dynamics and estimators. @abberior.rocks users can directly simulate sequence files.

GitHub - ries-lab/SimuFLUX: A comprehensive simulator for MINFLUX experiments. A comprehensive simulator for MINFLUX experiments. - ries-lab/SimuFLUX

These and many other simulations are covered in the paper. Example notebooks for each simulation are provided as part of the code base, and on Google Colab (see github.com/ries-lab/Sim...). We hope the community will find this useful and contribute their own simulated examples using this package.

For single molecule tracking, we optimized laser power, pattern size, photon limit and pattern dwell time to increase the measurable diffusion coefficient by 70% over that captured by the standard Abberior tracking sequence.

We simulated DNA-PAINT imaging using an Abberior sequence file, and showed that quenched DNA-PAINT probes may yield better images than standard probes in MINFLUX.

Fluorophore flickering can create up to a tenfold increase in localization precision. We showed this can be mitigated by repeated scanning of a fluorophore.

Starting off simple: misalignment of the phase pattern that generates a donut degrades performance, while misalignment of the pinhole has little effect.

Evaluating MINFLUX experimental performance in silico MINFLUX is a super-resolution microscopy technique with remarkable resolution for imaging and tracking. Its optical resolution is well understood under idealized conditions, but because of system comp...

MINFLUX works well in theory, but system and sample imperfections can lead to suboptimal resolution. To address this, @jonasries.bsky.social and I developed SimuFLUX: www.biorxiv.org/content/10.1..., a realistic simulator to optimize MINFLUX experiments before samples go on the microscope.

Our manuscript on accelerating the acquisition rate in oblique plane microscopy (OPM) is online now:

opg.optica.org/boe/fulltext...

Our work addresses the issue that an OPM PSF is tilted, and as such it leaves a lot of "empty space" in Fourier space (FFT of experimental data on the right)... 1/n

Checking out the cherry blossoms at Votivkirche