Zach Marin
@zacsimile.bsky.social
hardware x software in microscopy | postdoc in Ries Lab @maxperutzlabs.bsky.social | http://zacsimile.github.io | 🇺🇸 in 🇦🇹 | he/him | views are graphical projections
Coffee stains: not just for furniture
☢️🔬 To make tissue structures of biological samples visible under the electron microscope, they are treated with a straining agent: uranyl acetate, which is highly toxic and radioactive. A research team from TU Graz has now found an alternative: ordinary espresso. 😀
www.tugraz.at/en/news/arti...
www.tugraz.at/en/news/arti...
Coffee as a Staining Agent Substitute in Electron Microscopy
Researchers at TU Graz have proven that espresso is a favourable alternative to the highly toxic and radioactive uranyl acetate in the analysis of biological samples.
www.tugraz.at
January 10, 2026 at 1:13 PM
Coffee stains: not just for furniture
Now out in @natcomms.nature.com: www.nature.com/articles/s41...! The latest GitHub commits/Colab notebooks enable simulation with 3D sequences.
January 9, 2026 at 12:59 PM
Now out in @natcomms.nature.com: www.nature.com/articles/s41...! The latest GitHub commits/Colab notebooks enable simulation with 3D sequences.
Reposted by Zach Marin
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
www.nature.com/articles/s41...
rdcu.be/eQVxt
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.
www.nature.com
November 21, 2025 at 3:00 AM
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
www.nature.com/articles/s41...
rdcu.be/eQVxt
Reposted by Zach Marin
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
doi.org/10.1101/2025...
#Microscopy #CellBiology #OI-DIC #SMLM
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...
doi.org
October 16, 2025 at 11:57 PM
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
doi.org/10.1101/2025...
#Microscopy #CellBiology #OI-DIC #SMLM
Reposted by Zach Marin
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...
www.biorxiv.org/content/10.1...
October 6, 2025 at 5:52 PM
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...
www.biorxiv.org/content/10.1...
Reposted by Zach Marin
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...
www.nature.com/articles/s41...
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
www.nature.com
September 30, 2025 at 6:17 PM
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...
www.nature.com/articles/s41...
Reposted by Zach Marin
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
October 2, 2025 at 11:37 AM
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
Reposted by Zach Marin
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
September 30, 2025 at 4:25 PM
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
Reposted by Zach Marin
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
September 28, 2025 at 2:15 PM
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
Reposted by Zach Marin
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...
www.biorxiv.org/content/10.1...
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...
www.biorxiv.org
August 7, 2025 at 1:00 PM
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...
www.biorxiv.org/content/10.1...
Reposted by Zach Marin
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...
August 21, 2025 at 8:16 PM
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...
Reposted by Zach Marin
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
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...
rdcu.be
August 6, 2025 at 3:40 AM
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
Reposted by Zach Marin
🚨 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
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
July 31, 2025 at 8:56 AM
🚨 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
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
Reposted by Zach Marin
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
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.
www.nature.com
July 14, 2025 at 7:38 AM
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
Reposted by Zach Marin
Good news I've fixed the worst thing about Europe
June 29, 2025 at 4:56 PM
Good news I've fixed the worst thing about Europe
Reposted by Zach Marin
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.
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.
![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.](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:uf4m7zlmcjlg2biwn4s2k32y/bafkreibozn5fz6sgeksqrz3vmy6uiydtnvwmb5my7r3xecko2erokryn3a@jpeg)
![(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.](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:uf4m7zlmcjlg2biwn4s2k32y/bafkreielty6fex37xy4caechbw5ebo3eypyiyvxxhkigeazd5gmy6tvlay@jpeg)
June 17, 2025 at 11:09 AM
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.
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.
Reposted by Zach Marin
🚨🔬💗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...
pubs.aip.org/aip/apr/arti...
April 25, 2025 at 5:21 PM
🚨🔬💗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...
pubs.aip.org/aip/apr/arti...
Tiny yellow bird waiting at the metro stop this morning
April 25, 2025 at 6:05 AM
Tiny yellow bird waiting at the metro stop this morning
New work from Qiuqiang Zhan. Nonlinear multiphoton excitation eliminates side lobes in 4Pi, achieves 26 nm axial resolution: www.nature.com/articles/s41...
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...
www.nature.com
April 24, 2025 at 12:37 PM
New work from Qiuqiang Zhan. Nonlinear multiphoton excitation eliminates side lobes in 4Pi, achieves 26 nm axial resolution: www.nature.com/articles/s41...
Reposted by Zach Marin
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.
April 10, 2025 at 1:38 PM
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.
Reposted by Zach Marin
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:
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
academic.oup.com
April 9, 2025 at 3:47 PM
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:
Reposted by Zach Marin
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.
April 9, 2025 at 4:45 PM
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.
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.
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...
www.biorxiv.org
April 9, 2025 at 1:26 PM
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.
Reposted by Zach Marin
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
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
April 2, 2025 at 6:21 PM
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
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
March 30, 2025 at 1:00 PM
Checking out the cherry blossoms at Votivkirche