Andreas Müller

SynapseNet is a deep learning based software tool that automates the segmentation of vesicles, mitochondria, synaptic compartments, and the active zone. This is visualized in three panels. On the left, a section of an electron tomogram with a synaptic compartment densely filled with vesicles, which appear as round structures with dark boundary and light body in the image, is shwon. The top right panel shows the segmentation result of vesicles, visualized by masks with an individual color per vesicle and outlines for the segmented compartment (red) and active zone (blue). The bottom right panels shows a 3D rendering of the segmentation with vesicles shown as yellow spheres.

Are you studying synapses in electron microscopy? Tired of annotating vesicles? We have the tool for you! SynapseNet implements automatic segmentation and analysis of vesicles and other synaptic structures and has now been published:
www.molbiolcell.org/doi/full/10....

Expanded mouse olfactory bulb imaged with fluorescence at 20-50 nm resolution!

Ingenious concept - light sheet on serial sections by photo-etching the expanded hydrogel, layer by layer.

Photo-sectioning is quite slow, and the volumetric images are insanely large and complex, but the data look wonderful.

www.science.org/doi/10.1126/...

Poster of the 100-year history of The Company of Biologists.

1925: On this date, 100 years ago, The Company of Biologists is founded by George Parker Bidder III. Throughout today, we will be posting some of our key milestones. Read more about the past 100 years at bit.ly/3WnTVA1.

I found these immune cells just finished mitosis but their midbody is still yet to be resolved. How cool? If you zoom in to the midbody, you can see its classical shape just like in the textbooks. I love these little details.

Join us *next Monday*!
#CrickXrays25
X-ray #nanoimaging of biological tissues

🇬🇧🌐 @crick.ac.uk & online
tinyurl.com/crickxrays25

Sponsored by @dectris.bsky.social, @webknossos.org and @biologists.bsky.social and backed by @brukercorporation.bsky.social and Histomography

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...

🪰 A team of researchers has unveiled the complete connectome of a male fruit fly central nervous system—a seamless map of all the neurons in the brain and nerve cord of a single male fruit fly and the millions of connections between them.
🔗 https://hhmi.news/4o3EJnk

I’m happy to share some plugins I’ve been developping this summer: "Channels and Contrast" and LUTs Manager!
I can’t find new bugs and ideas by now so I need your help to please test them in your machines and report bugs, feedbacks and ideas! forum.image.sc/t/looking-fo...

Check the live stream of the Göttingen Expansion Forum 2025 if you're interested! I think the link changes every day will try to update. Program is here (pdf link): www.rizzoli-lab.de/wp-content/u...

To me the most exciting part is the exploration. Finding new connections between cells and figuring out what role they play in signaling.

Thank you. That's a very good question. It definitely opens new lines of research. Next, we need to find out what these connections actually do and if they change in diabetes. Then we look for ways to restore their function.

The Microscopists | Robert Haase (Leipzig University) We're thrilled to bring you the latest episode of The Microscopists, this time featuring Robert Haase, Lecturer and Training Coordinator at Leipzig University. In this episode, Robert chats about t...

Oh yes-the one and only Robert Haase @haesleinhuepf.bsky.social
From #GrandTheftAuto to the impact AI is having on #bioimaging.
+the challenges of creating AI courses for bioimage analysis, & his unique perspective as a programmer-turned-biologist.
Stream- bit.ly/microscopist...
@globias.bsky.social

Our new preprint is up! This is the main postdoc work of @wiesner-t.bsky.social focusing on exocytosis along the axon shaft and its regulation by the sub membrane actin-spectrin scaffold: www.biorxiv.org/content/10.1...
Read the thread below for a summary of our findings 🧵1/11

I wrote an article summarizing our recent findings of beta cell cilia - neuron contacts. It was fun to elaborate a bit on the exploration of #openaccess #volumeEM datasets: analyticalscience.wiley.com/content/arti...

CLEM-Reg: an automated point cloud-based registration algorithm for volume correlative light and electron microscopy - Nature Methods CLEM-Reg automates the three-dimensional alignment of volume correlative light and electron microscopy datasets by leveraging probabilistic point cloud registration techniques for fast and accurate re...

Super happy to see CLEM-Reg out in @natmethods.nature.com! A short thread on the algorithm behind it and how to try it out for yourself🧵(1/9)

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

Our new preprint is about the airway epithelium microtubule network, cilia, basal body protein composition, averaging of volumetric fluorescence data, and expansion microscopy.
Four years of very hard work from our very talented Emma van Grinsven. www.biorxiv.org/content/10.1... (1/N)

It's TODAY! Join us at the #VirtualPub for a talk by Rene' In't Zandt on “Metabolic MR Imaging in an experimental and clinical setting”
Hope to see you there!
🕐 13:00 CEST
More information ⤵️
www.eurobioimaging.eu/our-events/v...

We are all super happy and proud to see our work on the function and evolution of the #cephalic #furrow published in @nature.com. Let me say a few things about the background and history of this work on the #Evolution_of_Morphogenesis (1/12)

We have a fully funded 3y postdoc position open!!!! Come join us @mpi-cbg.de and @poldresden.bsky.social to understand the role of Membranes in Controlling Biogenic Crystallization :) this is part of our #HFSP funded project with @noemijimenezrojo.bsky.social and @vmonje.bsky.social! Applications👇

Amazing! Congratulations!

Trouble imaging actin in ExM? Meet HAK-Actin, a probe for U-ExM, cryo-ExM & iU-ExM. Enables post-expansion labeling for max signal. www.biorxiv.org/content/10.1...
Soon at @spirochrome.com
Led by O.Mercey and @lreymond.bsky.social, in collab with @dudinlab.bsky.social and @marinelap.bsky.social

A realistic phantom dataset for benchmarking cryo-ET data annotation - Nature Methods A standardized, realistic phantom dataset consisting of ground-truth annotations for six diverse molecular species is provided as a community resource for cryo-electron-tomography algorithm benchmarki...

Better ML for cryo-ET starts with better benchmarks.

We built a phantom cryo-ET dataset (~500 tomograms) + hosted a Kaggle challenge.

The result: community models beat expert tools.

Read more in the @natmethods.nature.com article that just came out:
🔗 doi.org/10.1038/s415...

#PhDstudent position in our lab – come join us to study epithelial:non-epithelial cell-cell interactions in mammalian tissues. We provide thorough training & an awesome team!
Apply by Sept. 16: shorturl.at/o9vzd
#epithelia #cellbiology #nextgenerationPhD #cellcellcommunication @hetcci.bsky.social

📢We're #hiring Group Leaders!

Apply to lead a lab at Janelia & advance biology using theory, computational modeling & machine learning.

🔹5-year renewable appointment
🔹Pioneer new tools & approaches
🔹Collaborate across disciplines

Apply by Nov. 4👉 https://janelia.link/groupleader

🧬🔬🧪 🎉 Our team at @czbiohub is thrilled to share TWO companion papers out today in @NatureMethods!
📦 Ultrack — robust, scalable nD cell tracking
🌐 inTRACKtive — a beautiful, open-source web viewer for lineage exploration
Let’s dive in! 👇
www.nature.com/articles/s41...
www.nature.com/articles/s41...

Out today in @nature.com: Together with the Honigmann, Shevchenko, Drobot and Hof labs, we present a general workflow for imaging the localization and transport of individual lipids in cells and mapping their metabolism.
www.nature.com/articles/s41...

Repost appreciated:
Open #PhDposition in structural virology in my group! Join us in Umeå, Sweden to uncover how arboviruses remodel infected cells. In situ #cryoET and #cryoEM combined with #virology, #cellbiology, and #biophysics.
Deadline 7 September. More info: www.carlsonlab.se/join/

Ctenophores possess a unique aboral organ that acts as a multisensory center, controlling complex behaviors. We’ve now created a ctenophore model integrated with our 3D volume EM data. Puts it into perspective.

Check out our recent work here: www.biorxiv.org/content/10.1...

#ctenophores #volumeEM

Don't miss the insights on image analysis and image analysts from @bethcimini.bsky.social! Happening on 🗓️ Thursday, July 31 at 5 pm CEST and 🗓️ Friday, August 1 at 8-9 am CEST.
Great online event with the @globalbioimaging.bsky.social community.
Registration link below ⤵️