Joachim Fuchs

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/...

2x Preprint drop!!! Mitochondrial pearling has arrived!
“The Biophysical Mechanism of Mitochondrial Pearling”.
“Pearling Drives Mitochondrial DNA Nucleoid Distribution” 1/10
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...

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...

Thanks to all the followers on @bsky.app if you’re a scientist please also follow the lab account @hassanbraindevlab.bsky.social for updates on our work minus all the personal/political opinions 😃

Hello Bluesky! I am an engineer/scientist currently working at the MRC LMB in Cambridge UK. During my PhD I developed new imaging technologies to shed light on the dynamics of living cells e.g. here is a movie of 6 organelles in live human cancer cells. Follow for more updates! #science #biology

‪Derivery Lab - MRC LMB‬ ‪@deriverylab.bsky.social‬ · 3m Congrats to Akaash, a postdoc in the lab, for winning the PhD Award from the Cambridge Centre for Physical Biology. His PhD research worked on the development of a multispectral imaging system capable of imaging up to 8 fluorophores similtaneously and tackling complex biological questions with this! Photograph of Akaash in posed infront of a computer monitor with a colourful cell imaged using his multispectral camera tree which is to the right of him. ALT Derivery Lab - MRC LMB ‪@deriverylab.bsky.social‬ An overview of Akaash's multispectral camera tree can be seen in the graphical abstract (which you can read more about here: www.physbiol.cam.ac.uk/prizes ). Peek at some colourful cells! 1a) Schematic of multispectral imaging hardware, b) photo of multispectral imaging hardware. 2a) Raw recorded data, b) emission spectra of fluorophores used in sample, c) unmixed data using novel algorithm, d) merge of data in c, e-f) other examples of simultaneous multispectral live cell imaging ALT December 11, 2024 at 11:20 AM Home Search Notifications Chat Feeds Lists Profile Settings Getting started Like 10 posts Teach our algorithm what you like Follow 7 accounts Bluesky is better with friends! Discover Following Extracellular Vesicles More feeds Feedback · Privacy · Terms · Help 1a) Schematic of multispectral imaging hardware, b) photo of multispectral imaging hardware. 2a) Raw recorded data, b) emission spectra of fluorophores used in sample, c) unmixed data using novel algorithm, d) merge of data in c, e-f) other examples of simultaneous multispectral live cell imaging

An overview of Akaash's multispectral camera tree can be seen in the graphical abstract (which you can read more about here: www.physbiol.cam.ac.uk/prizes ). Peek at some colourful cells!

Here's a #BIAToolTip for the weekend! As Tuco says in the movie, there are two kinds of processing for image quantification in the world - there's processing for intensity measurement, and there's processing for segmentation.

Know which way you'll go before choosing filters!

#bioimageanalysis

This is a good recommendation. In addition, for bar plots or other plots where you're coloring large areas, add some transparency. The viridis colors are too dark and saturated for large areas. They were designed for points and lines(*).

Compare left versus right.

YouTube video by I2K Conference Segment Anything for Microscopy

You can now watch the I2K video tutorial on #micro-sam by @anwaiarchit.bsky.social on YouTube: www.youtube.com/watch?v=dxjU... Check it out for an in-depth explanation for how to use our tool to segment your microscopy images.

Labkit - Intuitive Pixel Classification in Fiji The ImageJ wiki is a community-edited knowledge base on topics relating to ImageJ, a public domain program for processing and analyzing scientific images, and its ecosystem of derivatives and variants...

Seriously, for 3D segmentation, Labkit is wonderful.

Check it out (imagej.net/plugins/labk...)

Virtual I2K Flyer notifying that the Recordings are available on the I2K YouTube channel: https://www.youtube.com/@I2KConference

Happy #MicroscopyMonday!

The recordings of the #Virtual #I2K2024 workshops are available now
tinyurl.com/VirtualI2K20...

Thanks to all who presented!

Please re-share! 2022 and 2023 content available too:
www.youtube.com/@I2KConference

The brand new `legendry` package by @teunbrand.bsky.social takes ggplots2 guides to the next level 🤩

teunbrand.github.io/teunbrand_bl...

YouTube video by The Company of Biologists FocalPlane features... reproducibility in imaging

ICYMI: The October FocalPlane features… webinar included talks from @helenajambor.bsky.social (‘How not to lie with image data’) and Kota Miura ('Reproducible bioimage analysis for ensuring #scientificintegrity').

Watch the recording at
bit.ly/4fyB2SU

#PublicationIntegrityWeek #COPE