Mostafa Aakhte
@aakhte.bsky.social
Postdoc at the University of Göttingen (@huiskenlab), a physicist with an interest in Light-sheet microscopy, computer science, and developmental biology.
📝 https://www.nature.com/articles/s41587-025-02882-8
📝 https://www.nature.com/articles/s41587-025-02882-8
Pinned
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
🎉 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...
🔗 Read the full article:
www.nature.com/articles/s41...
Reposted by Mostafa Aakhte
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....
November 18, 2025 at 7:59 AM
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....
Reposted by Mostafa Aakhte
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
#lightsheet
#isotropic
#cochlea
November 20, 2025 at 9:20 PM
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
#lightsheet
#isotropic
#cochlea
Reposted by Mostafa Aakhte
For technical details see the following post:
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
www.nature.com/articles/s41...
#microscopy #lightsheet
November 16, 2025 at 2:47 PM
For technical details see the following post:
Reposted by Mostafa Aakhte
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!
Huge kudos to Max Hess for this PhD milestone! 💪
@lucaspelkmans.bsky.social shorturl.at/cO0u7
Let's zoom in!
October 29, 2025 at 2:20 PM
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!
Huge kudos to Max Hess for this PhD milestone! 💪
@lucaspelkmans.bsky.social shorturl.at/cO0u7
Let's zoom in!
Reposted by Mostafa Aakhte
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.
www.nature.com
November 16, 2025 at 2:45 PM
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...
🎉 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...
🔗 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
November 14, 2025 at 9:27 PM
🎉 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...
🔗 Read the full article:
www.nature.com/articles/s41...
Reposted by Mostafa Aakhte
Reposted by Mostafa Aakhte
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
www.nature.com/articles/s41...
#microscopy #lightsheet
November 14, 2025 at 4:41 PM
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
www.nature.com/articles/s41...
#microscopy #lightsheet
Reposted by Mostafa Aakhte
Research Briefing: High-speed isotropic light-sheet microscopy www.nature.com/articles/s41...
rdcu.be/ePWjG
rdcu.be/ePWjG
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...
www.nature.com
November 14, 2025 at 3:04 PM
Research Briefing: High-speed isotropic light-sheet microscopy www.nature.com/articles/s41...
rdcu.be/ePWjG
rdcu.be/ePWjG
Reposted by Mostafa Aakhte
Isotropic, aberration-corrected light sheet microscopy for rapid high-resolution imaging of cleared tissue - @huiskenlab.bsky.social go.nature.com/4odcS49
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.
go.nature.com
November 13, 2025 at 3:34 PM
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
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
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...
www.biorxiv.org
November 8, 2025 at 3:18 PM
Hybrid Solid-Liquid Optics Enable Scalable, High-Resolution, Multi-Immersion Light-Sheet Microscopy
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Mostafa Aakhte
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/
nikonsmallworld.com/
October 15, 2025 at 7:41 PM
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/
nikonsmallworld.com/
Reposted by Mostafa Aakhte
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...
-> 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...
October 13, 2025 at 12:44 AM
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...
-> 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...
Reposted by Mostafa Aakhte
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/
@spp2205.bsky.social @sfb1528.bsky.social @rtg2906-curiosity.bsky.social
@uni-goettingen.de events.gwdg.de/event/1099/
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...
events.gwdg.de
October 13, 2025 at 3:38 PM
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/
@spp2205.bsky.social @sfb1528.bsky.social @rtg2906-curiosity.bsky.social
@uni-goettingen.de events.gwdg.de/event/1099/
Reposted by Mostafa Aakhte
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.
Here it is! Postdoctoral position to identify the progenitors sensory organs in the regenerating legs of Parhyale
apply here: www.averof-lab.org/pages/tracman
1/3
apply here: www.averof-lab.org/pages/tracman
1/3
We've just been awarded a grant to study the cellular basis of regeneration – to track the progenitors of sensory organs in the context of leg regeneration, in our favourite crustacean tinyurl.com/parhyale, based on live imaging and cell tracking. The project involves some cool collaborations... 1/3
October 3, 2025 at 3:32 PM
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.
Reposted by Mostafa Aakhte
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:
September 15, 2025 at 8:42 AM
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:
Reposted by Mostafa Aakhte
The Huisken lab is now on Bluesky @huiskenlab.bsky.social - follow us for updates on our activities!
September 15, 2025 at 3:34 PM
The Huisken lab is now on Bluesky @huiskenlab.bsky.social - follow us for updates on our activities!
Reposted by Mostafa Aakhte
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.
September 15, 2025 at 3:27 PM
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.
Reposted by Mostafa Aakhte
#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...
github.com/haesleinhuep...
June 1, 2025 at 10:57 AM
#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...
github.com/haesleinhuep...
Reposted by Mostafa Aakhte
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!
May 19, 2025 at 1:10 PM
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!
Reposted by Mostafa Aakhte
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
Reposted by Mostafa Aakhte
Thermal Lensing Effects in Light-Sheet Microscopy
arxiv.org/abs/2504.02969
arxiv.org/abs/2504.02969
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...
arxiv.org
April 10, 2025 at 11:08 PM
Thermal Lensing Effects in Light-Sheet Microscopy
arxiv.org/abs/2504.02969
arxiv.org/abs/2504.02969
Reposted by Mostafa Aakhte
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...
amsikking.github.io/microscope_o...
February 25, 2025 at 5:06 PM
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...
amsikking.github.io/microscope_o...
Reposted by Mostafa Aakhte
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!
-> 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!
February 22, 2025 at 3:53 PM
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!
-> 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!
Reposted by Mostafa Aakhte
Remote refocus (RR) strikes again! ;)
Congrats to @aakhte.bsky.social and team on their interesting blend of opto-mechanical innovations!
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
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
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...
www.biorxiv.org
February 22, 2025 at 6:59 PM
Remote refocus (RR) strikes again! ;)
Congrats to @aakhte.bsky.social and team on their interesting blend of opto-mechanical innovations!
Congrats to @aakhte.bsky.social and team on their interesting blend of opto-mechanical innovations!