@joachimfuchs
Postdoc Hiesinger-Lab (FU Berlin) working with #Drosophila brain development (https://lab.flygen.org) previously PhD Eickholt Lab (Charité Berlin) | Filopodia & AxonBranching & Synapse formation | FijiSc | R | DataViz | UltimateFrisbee | he/him
New Hiesinger Lab paper! Melinda Kehribar et al. show how Flies preserve the spatial organization of visual input through axonal projections into the brain. A temporal gradient and two adhesive forces ensure a retinotopic map without a target-derived mechanism.
#neurosky #neuroskyence #Drosophila
On the publication bias discourse, I regret that metascience has become a source of decontextualized, low-res, bean-counting-focused `science is in crisis' narratives. It is largely uncurious abt science, desperately lacking in theory & measurement. I'll quote a few takes I liked & add my thoughts🧵
How do cells orchestrate themselves to achieve a directional movement as a group?
Hi, I’m @sayukihirano.bsky.social. In this thread, I’ll highlight key mechanisms of how cells communicate with each other to perform directional collective migration.
To all lipid-curious cell biologists: check out this comprehensive overview of lipid-based methods by @gerryhammond.bsky.social and colleagues in @jcb.org — a school of Babel fish for #lipidtime:
rupress.org/jcb/article/...
“adoption of AI in science presents what seems to be a paradox: an expansion of individual scientists’ impact but a contraction in collective science’s reach, as AI-augmented work moves collectively towards areas richest in data...
I am very happy (and a bit scared) to present to you what we have been working on over the last 4 years. This manuscript is exactly what I dreamt of when I started the lab and I could not be happier and prouder of the outcome!
Won best thesis award with this video! 4 years of research and play in 3 minutes :')
youtu.be/so0fPlK1-LM
On the left, the image shows a schematic of a fly head, ring neurons and EPG neurons together with some calcium imaging frames. On the right is a photo of a fly on a ball in virtual reality and another schematic of a VR system.
📢 Join us, the Haberkern lab, @uni-wuerzburg.de for a postdoc studying neural circuit mechanisms of navigation. You’ll spearheading neurophysiology experiments on our brand new 2P!
⏳ Apply by 28th February 2026
Details: www.haberkernlab.de/docs/ENPostd...
#neuroscience #academicjobs #postdoc
We just released a new major version of TrackMate (v8), the cell and organelle tracking plugin of Fiji.
It ships many new features, detailed below, but that are articulated around the following:
Finally, the first public release of #BigVolumeBrowser, so after teasers, you can try it yourself. For details, please check the announcement post (1/2)
forum.image.sc/t/bigvolumeb...
This #microscopymonday is a cleaning day. Watch how a #microglia cell mops up and phagozytoses debris and junk in a very messy neuronal co-culture. BTW, it was a proper cleaning job → the neurons made it and formed nice networks
Phase contrast imaging started at DIV1. One frame per 20 min.
Job alert!
We are looking for a bioimage analysis to work in an image analysis core facility in beautiful Paris. Can I ask you to share this opportunity with your networks?
See also on the forum:
forum.image.sc/t/research-e...
BioImage analysis friends - King's are recruiting for a full-time, permanent facility position! Come and work with fun microscopes and fun people (and me!) - please share! www.kcl.ac.uk/jobs/126345-...
Reconstructing long-range axons from dense brain images is tough.
This study introduces a novel method that separates axon identification from global statistical rules, showing big improvements over existing tools for mapping neuronal projections.
buff.ly/OBKr9cM
Figure legend: Categories and capabilities of smart microscopy systems integrating real-time image analysis and feedback control. Top: Smart microscopy workflows can be classified based on the driving logic behind decision-making: Event-driven (reacting to rare biological events), Outcome-driven (using feedback-control to steer biological systems toward a desired state), Quality-driven (optimizing signal quality or imaging metrics), and Information-driven (guided by models that predict which measurements/perturbations will yield the most informative data). Middle: Central feedback loop between the microscope and an image analysis system, which continuously exchanges images and commands to guide acquisition dynamically. Bottom: Key control actions enabled by smart microscopy: adjusting imaging modality (e.g. switching from brightfield to fluorescence, adjusting sampling rate), repositioning the field of view (e.g. tracking, drift correction), optimizing acquisition settings (e.g. adaptive optics), and performing photomanipulation (e.g. FRAP, ablation, optogenetics).
🔬🧠 Our paper on smart microscopy & the issue of interoperability! www.biorxiv.org/content/10.1... LONG THREAD WARNING: Smart microscopy uses real-time image analysis to automatically guide the acquisition or perturbation of the sample (closed feedback-control loop). Many applications exist:
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...
Our bryozoan paper is out in @genomeresearch.bsky.social! Led by @tomlewin.bsky.social, we report genome shuffling across the phylum and synteny evidence for the Lophophorata hypothesis. Grateful to John Bishop @thembauk.bsky.social and the DToL project for sharing openly!
doi.org/10.1101/gr.2...
FlyBase needs your help! We ask that European labs continue to contribute to Cambridge, UK FlyBase, whereas US and other non-European labs can contribute to US FlyBase. For more information and how to donate: wiki.flybase.org/wiki/FlyBase...
A reminder you/your lab can support FlyBase at Cambridge through the following link. Every bit helps. Please share if you yourself can't donate.
www.philanthropy.cam.ac.uk/give-to-camb...
Reminder that all three books I've co-authored are freely available online for non-commercial use (and the fourth will be, too)
Adapted from Fig. 1 from Kadiyala et al 2025.
Introducing five concepts from dynamical systems to decode developmental regulatory mechanisms, have a read! @perez-carrasco.bsky.social @roederlab.bsky.social @mpipz.bsky.social This effort started in a morphogenesis meeting @kitp-ucsb.bsky.social in 2023. journals.biologists.com/dev/article/...
I read and re-read the paper and talked to some on the experienced editorial staff.
My conclusion was that there were not sufficient reasons to retract the paper. The evidence was much weaker than was needed to fully support the claims. but this was true to some degree for many papers.
9/n
At this point, I might as well --
Here's an infographic showing different ways to include age as a predictor. The top shows two extremes, just as a plain old numerical predictor (imposes linear trajectory) vs. categorical predictor (imposes nothing whatsoever). And then three solutions in between!
The "reproducibility crisis" in science constantly makes headlines. Repro efforts are often limited. What if you could assess reproducibility of an entire field?
That's what @brunolemaitre.bsky.social et al. have done. Fly immunity is highly replicable & offers lessons for #metascience
A 🧵 1/n
How can we reform science? I have some ideas. But I am not sure you’ll like them, because they don’t promise much. elevanth.org/blog/2025/07...
Some rough design guidelines* 1. Match effectiveness with importance 2. Avoid ambiguity 3. Locality is king / eyes beat memory 4. Establish viewing order 5. Layer, layer, layer 6. When in doubt, grid 7. Treat visual attributes like adjectives * These guidelines are drawn largely from my experience + personal preferences + the literature. Design is messy, these are not perfect, others will disagree with me, etc. Caveat emptor.
These are the design guidelines I teach. From halfway through this deck: www.mjskay.com/presentation...
These days (for academic vis) I'd add "ensure natural visual operations correspond to meaningful operations in data space". Need to make slides for that.
I gave in! After students asking for it, I now made a simple figure design checklist.
To help all scientists w/o graphic skills create clear, accessible, and truthful charts!
-> Out in @nature Cell Biology: rdcu.be/erwl4
#DataVisualization #PhD #SciComm
Thx for review @bethcimini.bsky.social + 2
The hunt for a soulmate can be hard work. Neurons in the developing Drosophila antennal lobe simplify the problem by turning a 3D search into a 1D one.
By @callimcflurry.bsky.social
#neuroskyence
www.thetransmitter.org/developmenta...
Out today in @natmethods.nature.com : Spotiflow, our transcript localization method for imaging-based spatial transcriptomics. Led by amazing PhD student @albertdm.bsky.social, joint work w @gioelelamanno.bsky.social at EPFL / @scadsai.bsky.social
www.nature.com/articles/s41...
rdcu.be/epIB7
#drosophila @flybase.bsky.social request emergency funding:
"As it stands, by the end of July, 2025, there will be no future updates to FlyBase, and in the worst case scenario access to the website will also be lost" => please donate!
www.philanthropy.cam.ac.uk/give-to-camb...
