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Mostafa Aakhte

@aakhte.bsky.social
137 followers 93 following 5 posts

Postdoc at the University of Göttingen (@huiskenlab), a physicist with an interest in Light-sheet microscopy, computer science, and developmental biology. 📝 www.nature.com/articles/s41587-025-…

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Reposted by Mostafa Aakhte
Huisken lab @huiskenlab.bsky.social · 25/09/2026
Roman’s article in Laborpraxis explores microfluidics for multiplexed super-resolution imaging and its potential integration with Flamingo (in German): tinyurl.com/laborpraxis @romantsukanov.bsky.social #Flamingo #microfluidics #SuperResolution #microscopy #DNAPAINT #multiplexing
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Shayan Shamipour @shamipourshayan.bsky.social · 20/09/2026
Excited to share that our **3D-4i multiplexed imaging method** is now out in @natcomms.nature.com 🎉 🔗 www.nature.com/articles/s41... Huge thanks to the reviewers and editor for their constructive feedback and smooth handling of the work!
nature.com
Multiplexed embryo profiling links cellular state to zygotic genome activation in single cells - Nature Communications
The protein landscapes that underlie multicellular self-organization remain challenging to characterize across intact embryos at high spatial resolution. Here, the authors present 3D-4i, a high-throug...
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Huisken lab @huiskenlab.bsky.social · 09/09/2026
Flamingo at #DZG2026 in Münster: Torben presents cleared tissue imaging of crustacean heart #morphology. @tgoepel.bsky.social @morphonews.bsky.social #Flamingo #LSFM #light-sheet
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Huisken lab @huiskenlab.bsky.social · 07/09/2026
Shape the future of light: PhD opportunities in photonics in the Huisken lab. Excellent research network. Apply through the Max Planck School of Photonics. Deadline 1 Dec 2026. www.photonics.school/ #LSFM #lightsheet #Flamingo
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Huisken lab @huiskenlab.bsky.social · 11/06/2026
Huisken lab is at #EED2026! @metteh-thorsager.bsky.social & @bekeloh.bsky.social will show how we use #Flamingo #light-sheet microscopy to address biological questions in the annelid #Platynereis, with imaging of the developing nervous system as an example (Platy Satellite Meeting & Poster P146).
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Huisken lab @huiskenlab.bsky.social · 30/04/2026
These tools are valuable both as general cell membrane markers for tracking individual cells during development, and as a way to visualise nervous system formation. A great resource for the Platynereis community and beyond! 🧬 #lightsheet #Flamingo #developmental biology #platynereis
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Huisken lab @huiskenlab.bsky.social · 30/04/2026
Happy to share our contribution to this new work led by @michalis-averof.bsky.social! @bekeloh.bsky.social and @metteh-thorsager.bsky.social tested membrane tags in the annelid Platynereis dumerilii — many reached the cell membrane, and several also label the developing nervous system in the larvae.
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Huisken lab @huiskenlab.bsky.social · 14/03/2026
Honored to have two images from our lab selected among the Top 5 Research Images of the Year in Göttingen 🎉 The images will be exhibited in Forum Wissen until 10 April 2026. www.forum-wissen.de/event/resear... #ForumWissen #ScienceIsAlsoArt
forum-wissen.de
Research Images of the Year! Opening and Exhibition – Forum Wissen
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Huisken lab @huiskenlab.bsky.social · 14/03/2026
The image, which Mette (@metteh-thorsager.bsky.social) named “Democratising Imaging of Life in the Ocean,” features the salp Thalia democratica. It was captured with our portable Flamingo light-sheet microscope at @biodev-vlfr.bsky.social in collaboration with Alexandre Alié. #Salp #LBDV
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Huisken lab @huiskenlab.bsky.social · 14/03/2026
Lisa’s picture (@lisma-ulb.bsky.social), named “Where Science meets Art,” shows a transgenic line of the annelid worm Platynereis dumerilii. These worms were kindly provided by Guillaume Balavoine (@balavoinelab.bsky.social). #PlatynereisDumerilii #Annelid Photo credit: Yourong Frank Wang
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Huisken lab @huiskenlab.bsky.social · 14/03/2026
Being portable, we could bring the Flamingo light sheet microscope to the exhibition opening to explain how we captured the Salp image. This event shows that scientific research also reveals the beauty of the organisms we study. #LightSheet #LSFM #PortableMicroscope #Flamingo Photo credit: YF Wang
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Huisken lab @huiskenlab.bsky.social · 10/03/2026
We advocate for model-guided, representative sampling and visualizations that make biological variation tangible.
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Uni Göttingen @uni-goettingen.de · 08/01/2026
Faster, clearer, deeper 3D imaging Researchers developed an innovative light sheet fluorescence microscopy platform, which means detailed scans of fine networks of nerves or blood vessels are possible faster: www.uni-goettingen.de/en/3240.html... #NatureBiotechnology: doi.org/10.1038/s415...
Image showing two different views of the cochlea of a human inner ear shown on a black background with bright, detailed turquoise images and violet colours. The image is very clear and detailed. It was created using the new light sheet fluorescence microscopy platform developed by researchers. 

The image is adapted from Aakhte, M. et al., Nature Biotechnology, DOI: 10.1038/s41587-025-02882-8; openly licensed via CC BY 4.0
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Uni Göttingen @uni-goettingen.de · 16/01/2026
Lichtblattmikroskope erstellen 3D-Scans von Geweben und Organen – erzeugen bei großen Proben aber unscharfe Bilder. Forschende haben eine Plattform entwickelt, die diese Hürde überwindet. Mehr erfahren: www.uni-goettingen.de/de/3240.html... #MBexC #UMG @mbexc.bsky.social @huiskenlab.bsky.social
Hörschnecke eines menschlichen Innenohrs sichtbar gemacht mit dem neuartigen Lichtblatt-Fluoreszenzmikroskop © Adaptiert nach Aakhte, M. et al., Nature Biotechnology, DOI: 10.1038/s41587-025-02882-8; lizensiert nach CC BY 4.0
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Frank @frankcko.bsky.social · 22/11/2025
Absolutely loved this paper. Really addresses my personal gripes of not having isotropic voxel size in microscopy imaging rdcu.be/eRgYm
rdcu.be
Isotropic, aberration-corrected light sheet microscopy for rapid high-resolution imaging of cleared tissue
Nature Biotechnology - A light-sheet microscope built from off-the-shelf components enables high-resolution clear tissue imaging.
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Reposted by Mostafa Aakhte
Constantin Pape @cppape.bsky.social · 18/11/2025
Preprint alert! CochleaNet, our framework for analyzing light-sheet data of the cochlea. It consists of three networks to segment spiral ganglion neurons, inner hair cells, and to detect synapses. See rendering of a full cochlea in the image, find the preprint at doi.org/10.1101/2025....
Rendering of a full cochlea (left) with three stains (PV, VGlut3, CTBP2) shown in three different colors (red, blue, cyan). The whole cochlea is a spiral shaped structure, with spiral ganglion neurons (SGNs) in the inner helix, labeled by PV and inner hair cells (IHCs) in the outer helix, labeled by Vglur3. The figure also shows zoom ins. The right hand side shows segmentation results for SGNs, IHCs (represented by colored masks) and synapse detections (represented by colored dots).
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Huisken lab @huiskenlab.bsky.social · 20/11/2025
Studying cochlear neuroanatomy demands imaging the entire cochlea at subcellular resolution. In our recent study (tinyurl.com/isotropicLSFM), we recorded the cochlea at isotropic resolution across the whole organ, laying the groundwork for what follows… #lightsheet #isotropic #cochlea
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Jan Wenzel @janwenzel.bsky.social · 16/11/2025
For technical details see the following post:
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Shayan Shamipour @shamipourshayan.bsky.social · 29/10/2025
Very happy to share our latest work extending iterative immunofluorescence to in toto imaging of early zebrafish embryos (3D-4i), integrated with a 3D-dedicated image analysis pipeline! 🐟🔬📊 Huge kudos to Max Hess for this PhD milestone! 💪 @lucaspelkmans.bsky.social shorturl.at/cO0u7 Let's zoom in!
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Jan Wenzel @janwenzel.bsky.social · 16/11/2025
I am happy to share a recent collaboration with @huiskenlab.bsky.social and @aakhte.bsky.social , who developed a great technique for performing fast and, above all, isotropic light-sheet microscopy. www.nature.com/articles/s41...
nature.com
Isotropic, aberration-corrected light sheet microscopy for rapid high-resolution imaging of cleared tissue - Nature Biotechnology
A light-sheet microscope built from off-the-shelf components enables high-resolution clear tissue imaging.
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Mostafa Aakhte @aakhte.bsky.social · 14/11/2025
🎉 I am very glad to share that our paper on the rapid isotropic light-sheet microscope has just been published in Nature Biotechnology @natbiotech.nature.com. 🔗 Read the full article: www.nature.com/articles/s41...
nature.com
Isotropic, aberration-corrected light sheet microscopy for rapid high-resolution imaging of cleared tissue - Nature Biotechnology
A light-sheet microscope built from off-the-shelf components enables high-resolution clear tissue imaging.
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Kevin Dean @kevin-dean.bsky.social · 13/11/2025
www.nature.com/articles/s41...
nature.com
Isotropic, aberration-corrected light sheet microscopy for rapid high-resolution imaging of cleared tissue - Nature Biotechnology
A light-sheet microscope built from off-the-shelf components enables high-resolution clear tissue imaging.
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Reposted by Mostafa Aakhte
Huisken lab @huiskenlab.bsky.social · 14/11/2025
Happy to see our paper “Isotropic, aberration-corrected light sheet microscopy for rapid high-resolution imaging of cleared tissue” in @natbiotech.nature.com – with Tobias Moser’s lab from @unimedizin-goe.bsky.social and @janwenzel.bsky.social www.nature.com/articles/s41... #microscopy #lightsheet
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Nature Biotechnology @natbiotech.nature.com · 14/11/2025
Research Briefing: High-speed isotropic light-sheet microscopy www.nature.com/articles/s41... rdcu.be/ePWjG
nature.com
High-speed isotropic light-sheet microscopy - Nature Biotechnology
Achieving uniform, isotropic sub-micrometer-resolution imaging at high speed across large, cleared tissues has been a major challenge for light-sheet microscopy. To address this, we developed a cost-e...
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Nature Biotechnology @natbiotech.nature.com · 13/11/2025
Isotropic, aberration-corrected light sheet microscopy for rapid high-resolution imaging of cleared tissue - @huiskenlab.bsky.social go.nature.com/4odcS49
go.nature.com
Isotropic, aberration-corrected light sheet microscopy for rapid high-resolution imaging of cleared tissue - Nature Biotechnology
A light-sheet microscope built from off-the-shelf components enables high-resolution clear tissue imaging.
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Mostafa Aakhte @aakhte.bsky.social · 08/11/2025
Hybrid Solid-Liquid Optics Enable Scalable, High-Resolution, Multi-Immersion Light-Sheet Microscopy www.biorxiv.org/content/10.1...
biorxiv.org
Hybrid Solid-Liquid Optics Enable Scalable, High-Resolution, Multi-Immersion Light-Sheet Microscopy
Modern biology increasingly depends on data-driven discovery, requiring scalable and affordable high-content 3D imaging across molecular to organ scales. Although tissue clearing, expansion microscopy...
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Reposted by Mostafa Aakhte
Huisken lab @huiskenlab.bsky.social · 15/10/2025
Our image of a sea squirt oozoid (Thalia democratica) was selected as an Image of Distinction in Nikon Small World. Imaged with the Flamingo microscope by @metteh-thorsager.bsky.social at @biodev-vlfr.bsky.social in Villefranche-sur-Mer. Salp sample courtesy of Alexandre Alie. nikonsmallworld.com/
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Alfred Millett-Sikking @amsikking.bsky.social · 13/10/2025
The future of High-Content Imaging has arrived. -> Ultra-fast 3D imaging of multi-well plates at high resolution using an air objective! See previous posts and the new miOPM preprint for details: doi.org/10.1101/2025...
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Huisken lab @huiskenlab.bsky.social · 13/10/2025
Huisken lab is attending Göttingen Cognition Forum: Curiosity & Interaction. Learn about our research... @spp2205.bsky.social @sfb1528.bsky.social @rtg2906-curiosity.bsky.social @uni-goettingen.de events.gwdg.de/event/1099/
events.gwdg.de
The Göttingen Cognition Forum: Curiosity & Interaction
We are pleased to announce the First Göttingen Cognition Forum: Curiosity & Interaction The conference brings together researchers from neuroscience, psychology, behavioral biology, computational scie...
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Huisken lab @huiskenlab.bsky.social · 03/10/2025
Postdoc opportunity in the Averof lab: a crustacean meets a flamingo—not on the menu, but in the light sheet. Track the origins of cells during leg regeneration in Parhyale hawaiensis using light sheet microscopy. Excited to be part of this interdisciplinary project. Details on how to apply below.
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James Manton @jamesdmanton.bsky.social · 15/09/2025
We present a simple method to easily increase the imageable depth of an expansion microscopy gel on a typical inverted microscope ten-fold, using some carefully placed FEP film and a water dipping objective lens:
A comparison of imaging an expansion microscopy hydrogel with a water dipping objective lens, using either eye gel as an immersion medium or a combination of Immersol W, water and a thin FEP film. In both cases, the sample is supported by a thin FEP film rather than a coverglass.
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Mette Handberg-Thorsager @metteh-thorsager.bsky.social · 15/09/2025
The Huisken lab is now on Bluesky @huiskenlab.bsky.social - follow us for updates on our activities!
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Huisken lab @huiskenlab.bsky.social · 15/09/2025
We brought our Flamingo microscope to the light sheet microscope course in Dresden (#LISH25). We captured extensive time-lapse recordings and are excited to share highlights from our experiments with Hydra and Zebrafish.
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Robert Haase @haesleinhuepf.bsky.social · 01/06/2025
#biabob 0.28.0 is out and it comes with support for OpenAI's codex-mini model. I also enabled its vision-support. With this, you can turn screenshots of user-interfaces into functional code - directly within your Jupyter notebook 🤯 github.com/haesleinhuep...
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Adam Glaser @adamkglaser.bsky.social · 19/05/2025
We are excited to share our development of a new 10X lens with NA=0.50 over a 7.2 mm FOV and a 35 mm working distance (water), fully corrected from 400-850 nm. This lens will power our upcoming ExA-SPIM "2" and is available for dissemination - please get in touch if interested!
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Reto Fiolka @retof.bsky.social · 02/04/2025
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
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Adam Glaser @adamkglaser.bsky.social · 11/04/2025
Thermal Lensing Effects in Light-Sheet Microscopy arxiv.org/abs/2504.02969
arxiv.org
Thermal Lensing Effects in Two-Photon Light-Sheet Microscopy
In light-sheet fluorescence microscopy (LSFM), the axial resolution is governed by the illumination beam profile, motivating the development of advanced beam-shaping techniques to enhance imaging perf...
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Alfred Millett-Sikking @amsikking.bsky.social · 25/02/2025
Microscope objectives can be confusing, and detailed specs (or even basic properties) are often hard to find. Here's an introductory resource to help new builders and instrument designers with the basics. It's a work in progress so feedback is appreciated: amsikking.github.io/microscope_o...
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Alfred Millett-Sikking @amsikking.bsky.social · 22/02/2025
To solve the collision problem in OPM (previous post), lower numerical aperture (NA) objectives with longer working distances were used: -> Here we show the pupils in a remote refocus (3 circles). The reduced NA in the downstream objectives loses light (yellow circle) and lowers the resolution!
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Mostafa Aakhte @aakhte.bsky.social · 22/02/2025
Thanks for the kind words, Alfred!
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Alfred Millett-Sikking @amsikking.bsky.social · 22/02/2025
Remote refocus (RR) strikes again! ;) Congrats to @aakhte.bsky.social and team on their interesting blend of opto-mechanical innovations!
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Adam Glaser @adamkglaser.bsky.social · 21/02/2025
Isotropic, aberration-corrected light sheet microscopy for rapid high-resolution imaging of cleared tissue www.biorxiv.org/content/10.1...
biorxiv.org
Isotropic, aberration-corrected light sheet microscopy for rapid high-resolution imaging of cleared tissue
Light sheet microscopy is the ideal technique for multiscale imaging of large and cleared tissues, and it is desirable to achieve the highest possible isotropic resolution across the entire sample. Ho...
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Mostafa Aakhte @aakhte.bsky.social · 22/02/2025
Thanks, Alain!
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Alain Chédotal @alainchedotal.bsky.social · 22/02/2025
Impressive & clever. A light-sheet microscope with isotropic resolution <1 μm. Uses a using a concave mirror to correct optical abberation and swipes the light sheet. Validated on mouse brain vasculature & cochlea . @aakhte.bsky.social Huisken lab www.biorxiv.org/content/10.1...
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Constantin Pape @cppape.bsky.social · 21/02/2025
Our first deposition of synaptic vesicles segmentations is now in the Cryo ET Portal! We segmented vesicles in over 50 tomograms to enable analysis of membrane proteins and more. cryoetdataportal.czscience.com/depositions/...
Synaptic vesicles segmented with SynapseNet.
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Mostafa Aakhte @aakhte.bsky.social · 21/02/2025
Looks incredible, congrats Constantin!
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Constantin Pape @cppape.bsky.social · 12/02/2025
After a long journey, Segment Anything for Microscopy is now published in Nature Methods! We significantly improve SAM for interactive and automatic segmentation in light and electron microscopy and build a user-friendly tool. www.nature.com/articles/s41...
Improvements in LM (top) and EM (bottom) of our micro-sam model (finetuned) compared to the default SAM model.
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