Mostafa Aakhte

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).

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....

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

For technical details see the following post:

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!

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.

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...

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.

🎉 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...

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.

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

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

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...

Research Briefing: High-speed isotropic light-sheet microscopy www.nature.com/articles/s41...
rdcu.be/ePWjG

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.

Isotropic, aberration-corrected light sheet microscopy for rapid high-resolution imaging of cleared tissue - @huiskenlab.bsky.social go.nature.com/4odcS49

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...

Hybrid Solid-Liquid Optics Enable Scalable, High-Resolution, Multi-Immersion Light-Sheet Microscopy
www.biorxiv.org/content/10.1...

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/

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...

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...

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/

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.

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:

The Huisken lab is now on Bluesky @huiskenlab.bsky.social - follow us for updates on our activities!

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.

#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...

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!

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

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...

Thermal Lensing Effects in Light-Sheet Microscopy
arxiv.org/abs/2504.02969

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...

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!

Thanks for the kind words, Alfred!

Remote refocus (RR) strikes again! ;)

Congrats to @aakhte.bsky.social and team on their interesting blend of opto-mechanical innovations!

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...

Isotropic, aberration-corrected light sheet microscopy for rapid high-resolution imaging of cleared tissue

www.biorxiv.org/content/10.1...

Thanks, Alain!

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...

Synaptic vesicles segmented with SynapseNet.

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/...