Joachim Fuchs

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.

Research engineer in Bioimage Analysis for the researchers of the inIdEx FORMULA Hi all 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? The position is in the Instit...

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 Specialist | King's College London

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

Which Kind of Science Reform What hope is there for science reform, if we can't agree on what to reform? Right now, principles are more important than practices.

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.

A checklist for designing and improving the visualization of scientific data Nature Cell Biology - Creating clear and engaging scientific figures is crucial to communicate complex data. In this Comment, I condense principles from design, visual perception and data...

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

How developing neurons simplify their search for a synaptic mate Streamlining the problem from 3D to 1D eases the expedition—a strategy the study investigators deployed to rewire an olfactory circuit in flies.

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 Genetic Database The Drosophila Genetic Database, FlyBase, is on the brink of collapse due to the sudden termination of the FlyBase NIH grant, which includes salaries for 5 literature curators based at the University ...

#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...

ok stats experts!
if we have measures in a timecourse, how would you capture whether different groups show a different pattern?

i guess the simple/obvious thing is t test on a given timepoint but this throws away all the info from multiple timepoints...

any link/tutorial you like? (pls rski)

Toward a probabilistic definition of neural cell types A classical view of cell type relies on a definite set of stable properties that are critical for brain functions. Single-cell technologies led to an …

@maheandria.bsky.social and I challenge the notion of a static and deterministic definition of a (neural) cell type and argue for its replacement by a multi parametric probabilistic definition in this perspective
sciencedirect.com/science/arti...

Introducing warpfield, an open source Python library for GPU-accelerated non-rigid 3D registration. Warps and aligns gigavoxel volumes within seconds (not hours). For 3D microscopy, region-to-region and cell-to-cell matching.
A collaboration with @mh123.bsky.social 🚀
github.com/danionella/w...

Sequential and independent probabilistic events regulate differential axon targeting during development in Drosophila melanogaster Nature Neuroscience - The developmental origin of behavioral individuality is unclear. The authors show that a temporal sequence of genetically encoded stochastic mechanisms explains variation in...

Hot off the press:
The excellent Maheva Andriatsilavo and colleagues show how a temporal sequence of stochastic molecular mechanisms allow the emergence of stereotyped individualised neuronal circuits. Just published in Nature Neuroscience:
rdcu.be/ek010

An idea for a workshop that you can run (or take yourself!) to teach "R for cell biologists". 🧪
quantixed.org/2025/01/20/g...

"Die Neurobiologie der Künstlichen Intelligenz": Vortrag im Rahmen der Dahlemer Wissenschaftsgespräche am 15. Januar um 18 Uhr. Eintritt frei.

📍Freie Universität Berlin, Forschungsbau SupraFAB, Altensteinstraße 23a, 14195 Berlin, Meeting Point Raum 201

▶️Infos: www.fu-berlin.de/presse/infor...

Images of Drosophila wings. Control wings expressing CRISPR components exclusively in the germline have normal morphology. Targeting the central hedgehog signaling component smoothened with Cas9 and either one or two sgRNAs results in wings of reduced size and missing and ectopic vein tissue (middle panels). Targeting smoothened with Cas12a+ and four sgRNAs results in very small wings without veins.

The power of Cas12a-enabled sgRNA multiplexing for gene disruption.

Today’s example: smoothened
1/3
#CRISPR #Drosophila

CellTracksColab is a platform that enables compilation, analysis, and exploration of cell tracking data Exploring large amounts of cell tracking data remains a challenge. This study presents CellTracksColab, a platform that provides a transformative solution for cell tracking analysis, combining cutting...

I am now adding a section "Manuscript preparation" in the material and methods of our manuscripts
See journals.plos.org/plosbiology/...

There are now 24 step-by-step guides, explaining how to create these ⬇️ data visualizations with R/ggplot2 - I hope this is a useful resource. Find them all here: joachimgoedhart.github.io/DataViz-prot...