Lightnews — Scholar-powered news

Reposted by Elena Nicolay

Peter O'Toole @yorkbioimaging.bsky.social · 26d

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

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...

bit.ly

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Elena Nicolay @enicolay.bsky.social · Sep 3

London moves into the spotlight for #NeuroGASTRO2025 🌈🌈 Meet me at poster AI-03 to talk about how we're shedding light on #ENS research 🐟🔬 💻

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Reposted by Elena Nicolay

Elnaz @mycroscopy.bsky.social · Aug 29

Just out of the oven

onlinelibrary.wiley.com/doi/10.1111/...

I’m so excited! Stay tuned for more posts about it and give it a read when you can🥰

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Robert Haase @haesleinhuepf.bsky.social · Jul 27

After we lost our beloved cat Pixel earlier this summer, we decided to increase our catabilities:
Please welcome Oskar (left) and Kiwi (right) #kittens 🐈🐈‍⬛️

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Reposted by Elena Nicolay

Possible Worlds Games @possibleworlds.bsky.social · Jul 13

Burnout is clinically understood as a combo of 6 factors—work overload, lack of control, insufficient rewards, breakdown in community, absence of fairness, & value conflicts—and only a fraction of it is under your control. Burnout is a systemic problem, so be kind to yourself and hard on the system.

Superdillin (Mirror your pronouns) @superdillin.bsky.social · Jul 13

Hey gang I've had to learn recently that the whole "burning out" thing is real so if you find yourself being panicked every waking second that you're not working on something, despite those seconds being very rare, you should maybe listen to the signals and take an intentional break before you crash

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Reposted by Elena Nicolay

Helmholtz Imaging @helmholtzimaging.bsky.social · Jul 10

Got questions about the #HelmholtzImaging Project Call?

Ask everything you need to know at our next info session on Thursday, July 17, 11:00 to 12:40 PM CEST. Learn how #HIFIS can support your project, too.

Details & registration 👉 events.hifis.net/event/2663/

@helmholtz.de #HIProject #imaging

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Reposted by Elena Nicolay

UFZ @ufz.de · Jul 10

Forschende unter Leitung des #UFZ haben #Nanoplastik in allen Tiefenzonen zwischen gemäßigter und subtropischer Zone im Nordatlantik gefunden. Massenmäßig ist die Menge vergleichbar mit dem, was bisher an #Mikroplastik gefunden wurde, schreiben sie im Fachmagazin @Nature. www.ufz.de/index.php?de...

Nature @nature.com · Jul 9

These plastic particles smaller than a human hair can pass through cell walls and enter the food web

go.nature.com/44TofaH

Millions of tonnes of nanoplastics are polluting the ocean

These plastic particles smaller than a human hair can pass through cell walls and enter the food web

go.nature.com

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Reposted by Elena Nicolay

The Company of Biologists @biologists.bsky.social · Jul 8

Looking for new #microscopy collaborations, organising speakers for a conference, assembling a committee?

Visit and join the @focalplane.bsky.social network to broaden your contacts and find those who may not come to mind.

focalplane.biologists.com/network

#Microscope #Imaging #CellBiology

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Reposted by Elena Nicolay

Guillaume Jacquemet @guijacquemet.bsky.social · Jun 27

Generate beautiful PDF of your manuscripts easily using Markdown. #RxivMaker is here. We hope it will supercharge your #preprints Mojo.

Ricardo Henriques @henriqueslab.bsky.social · Jun 27

🧑‍🔬📰🚀 #RxivMaker is here! A framework automating the creation of publication-ready scientific #preprints from simple Markdown. Goodbye manual formatting, and hello gorgeous manuscripts! A great adventure with @guijacquemet.bsky.social's lab

📜: zenodo.org/records/1575...
👨‍💻: github.com/HenriquesLab...

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Reposted by Elena Nicolay

German BioImaging @gerbi-gmb.de · Jun 25

🔬 YMIA is at the Helmholtz Imaging Conference 2025!
Elena from the core team presents a poster about the YMIA community — who we are, what we do, and how we connect early-career researchers in imaging and analysis.

She’s here to exchange ideas and meet you. Come say hi!

#HIConference2025 #BSIC2025

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Reposted by Elena Nicolay

Helmholtz Imaging @helmholtzimaging.bsky.social · Jun 25

Great vibes, exciting science! 🐟 Today, the #zebrafish community in @helmholtz.de met for the 1st time at #HIconference2025. We kicked things off with energy, ideas & tools for better zebrafish #imaging. Thanks to all who joined & our co-hosts @ufz.de & BER at @kit.edu!

#HelmholtzImaging #FAIRdata

Group photo, Zebrafish pre-conference workshop, HI Conference 2025

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Reposted by Elena Nicolay

Helena Klara Jambor @helenajambor.bsky.social · Jun 18

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

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...

rdcu.be

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Reposted by Elena Nicolay

Ethan Scott's Lab @ethanscottlab.bsky.social · Jun 16

ICYMI #zebrafish folks:

Fresh from ‪@lascholz.bsky.social‬ and Conrad Lee, we offer 4 models pre-trained with diverse fps and resolutions. Leandro’s done all of the clicking. Benefit from his suffering and plug straight into automated annotation of your videos!‬

www.biorxiv.org/content/10.1...

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Reposted by Elena Nicolay

Robert Haase @haesleinhuepf.bsky.social · Jun 15

If you seek for an AI coding buddy to review your code and provide umprompted feedback, try out _unprompted_! I hope it helps to identify issues in code early! 🖥️🤖💫
pip install unprompted
github.com/haesleinhuep...

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Reposted by Elena Nicolay

Helmholtz Imaging @helmholtzimaging.bsky.social · Jun 12

Helmholtz turns 30 – and shares 30 inspiring stories from across the @helmholtz.de.

Today’s spotlight: the Helmholtz Information & Data Science platforms – including #HelmholtzImaging, @helmholtzai.bsky.social, HIDA, HIFIS & HMC.

Read more 👇

#Helmholtz #Helmholtz30 #DataScience #imaging

Helmholtz-Gemeinschaft @helmholtz.de · Jun 12

How does data science accelerate research?
Through platforms, AI knowledge, and groundbreaking projects.
The Helmholtz Information & Data Science Framework enables this – from sustainable data management to AI applications in research."

Read more in our story! t1p.de/k1np9 #Helmholtz30

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Reposted by Elena Nicolay

Tamara Tal @tamaratal.bsky.social · Jun 12

Scott Glaberman, Chris Frey and I lay out why EPA's Office of Research and Development should be protected, not destroyed. Please share widely.

Dismantling EPA’s research office jeopardizes environmental safety, public health, and US competitiveness | PNAS www.pnas.org/doi/10.1073/...

PNAS

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...

www.pnas.org

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Reposted by Elena Nicolay

Tom Boissonnet @tom-bssnnt.bsky.social · Jun 5

A reason I go to conferences is to promote image data managment. I tend to repeat myself a little, so here's my elevator speech in memes.

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Reposted by Elena Nicolay

Rita Strack @ritastrack.bsky.social · Jun 3

Can you go from protein sequence to a generated image of protein localization? New work from the Uhler lab says yes, and it is generalizable to unseen proteins and more than one cell type. I'm excited for work moving us toward virtual cell models.

Nature Methods @natmethods.nature.com · May 13

PUPS - prediction of unseen proteins' subcellular localization - uses machine learning models to predict the localization of unseen proteins in unseen cell lines from sequence and cellular images.

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

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Reposted by Elena Nicolay

Mara Lampert @marabuuuu.bsky.social · May 16

Image normalization: trivial enough to automate, impactful enough to quietly sabotage your results.
Here’s a Jupyter notebook I wrote on how, why & when normalization matters, feedback 💛ly welcome.
👇

haesleinhuepf.github.io/BioImageAnal...

Image Normalization — Bio-image Analysis Notebooks

haesleinhuepf.github.io

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Elena Nicolay @enicolay.bsky.social · May 16

Do you work with large image datasets?
Discover our optimized workflows for efficient metadata annotation and #FAIR data management. 🔬💻

NFDI4BIOIMAGE @nfdi4bioimage.bsky.social · May 14

#FAIR workflows for image data management! 🧬
Riccardo Massei and team created workflows on #Galaxy to (semi-)automate metadata annotation of HCS images and transfer it to #OMERO & #IDR. Making large bioimage datasets FAIR and machine-readable.

👉 www.nature.com/articles/s41...

Elena Nicolay @enicolay.bsky.social · May 12

Please take a moment to appreciate the beautiful imaging art that was submitted this year 😍 (also, can you spot my image?)

Helmholtz Imaging @helmholtzimaging.bsky.social · May 12

🎉 Public Voting Now OPEN – #HelmholtzImaging Best Scientific Image Contest 2025

Choose your favorite(s) & cast your vote by May 30 👉 bit.ly/BSIC2025-Public-Voting

The award recipients will be announced at our conference on June 26.

#HIBestImage25 #HIConference25
@www.helmholtz.de

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Elena Nicolay @enicolay.bsky.social · May 12

Probably good to ask in the forum.image.sc 🤔
Good luck!

Image.sc Forum

Scientific Community Image Forum is a discussion forum for scientific image software sponsored by the Center for Open Bioimage Analysis (COBA).

forum.image.sc

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Reposted by Elena Nicolay

Maik Bischoff @maikbischoff.bsky.social · May 12

I am slowly loosing my mind over this #Fiji / #ImageJ plugin...

I want to use Noise2Noise, but it keeps giving me this error code 403... I checked the internet but couldn't find anything that helped me in this situation. I am sure swarm intelligence here knows the issue 😀

#cellbio #microscopy

Error code saying:
[INFO] Version of TensorFlow: TF 1.12.0 CPU
[ERROR] Could not create input stream:
java.io.IOException: HTTP connection failure, errorcode: 403
at org.scijava.io.http.HTTPHandle.result(HTTPHandle.java:192)
at org.scijava.io.http.HTTPHandle.in(HTTPHandle.java:93)
at org.scijava.io.handle.StreamHandle.read(StreamHandle.java:149)
at org.scijava.io.handle.DataHandle.read(DataHandle.java:446)
at org.scijava.io.handle.DataHandles.copy(DataHandles.java:246)
at org.scijava.io.handle.DataHandles.copy(DataHandles.java:191)
at org.scijava.io.handle.DataHandles.copy(DataHandles.java:151)
at org.scijava.download.DefaultDownloadService.lambda$download$1(DefaultDownloadService.java:108)
at org.scijava.task.DefaultTask.lambda$initFuture$0(DefaultTask.java:236)
at org.scijava.thread.DefaultThreadService.lambda$wrap$1(DefaultThreadService.java:233)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:750)
and so on...

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Reposted by Elena Nicolay

Jeff Thompson @echinerd.bsky.social · May 12

Interested in Developmental biology? Imaging? Marine invertebrate body plans? Then this three year postdoc in my group @sotonbiosciences.bsky.social is for you! Join our team to decypher how signalling molecules shape skeletal phenotype in juvenile sea urchins. jobs.soton.ac.uk/Vacancy.aspx...

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Elena Nicolay @enicolay.bsky.social · May 12

It's combining fun, peers and science - a great mix! 🔬🎉

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