Elena Nicolay
@enicolay.bsky.social
Doctoral Researcher at mTox lab, @ufz.de Leipzig 🧪🌊 | Intrigued by #EntericNervousSystem and #InnateImmunity in #Zebrafish
🐟🔬💻
🐟🔬💻
Pinned
Elena Nicolay
@enicolay.bsky.social
· Nov 22
Hi BlueSky! For my first #FluorescenceFriday, here's my intro 👋 I study how intestinal neurons and immune cells interact under environmental chemical exposure, using zebrafish larvae as model organism. Check out these #Macrophages and #EntericNeurons! 🐟✨
Reposted by Elena Nicolay
Bis jetzt war ja alles grau. Aus diesen riesigen Datensätzen können wir 3D Modelle der Zellen erstellen. Eins davon seht ihr hier (Erstellt von meiner Kollegin Deborah Schmidt). Wie wir von den Rohdaten zu diesen 3D Abbildungen kommen, werde ich euch diese Woche zeigen.
November 10, 2025 at 12:35 PM
Bis jetzt war ja alles grau. Aus diesen riesigen Datensätzen können wir 3D Modelle der Zellen erstellen. Eins davon seht ihr hier (Erstellt von meiner Kollegin Deborah Schmidt). Wie wir von den Rohdaten zu diesen 3D Abbildungen kommen, werde ich euch diese Woche zeigen.
Reposted by Elena Nicolay
Fluorescent micrograph of the enteric nervous system of a Pachon/surface hybrid cavefish. Credit to @pavaniperera.bsky.social. #ZebrafishZunday 🧪
November 9, 2025 at 5:09 PM
Fluorescent micrograph of the enteric nervous system of a Pachon/surface hybrid cavefish. Credit to @pavaniperera.bsky.social. #ZebrafishZunday 🧪
Reposted by Elena Nicolay
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
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
September 19, 2025 at 11:15 AM
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
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
London moves into the spotlight for #NeuroGASTRO2025 🌈🌈 Meet me at poster AI-03 to talk about how we're shedding light on #ENS research 🐟🔬 💻
September 3, 2025 at 6:24 PM
London moves into the spotlight for #NeuroGASTRO2025 🌈🌈 Meet me at poster AI-03 to talk about how we're shedding light on #ENS research 🐟🔬 💻
Reposted by Elena Nicolay
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🥰
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🥰
August 29, 2025 at 8:11 PM
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🥰
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🥰
Reposted by Elena Nicolay
After we lost our beloved cat Pixel earlier this summer, we decided to increase our catabilities:
Please welcome Oskar (left) and Kiwi (right) #kittens 🐈🐈⬛️
Please welcome Oskar (left) and Kiwi (right) #kittens 🐈🐈⬛️
July 27, 2025 at 7:43 AM
After we lost our beloved cat Pixel earlier this summer, we decided to increase our catabilities:
Please welcome Oskar (left) and Kiwi (right) #kittens 🐈🐈⬛️
Please welcome Oskar (left) and Kiwi (right) #kittens 🐈🐈⬛️
Reposted by Elena Nicolay
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.
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
July 13, 2025 at 11:10 PM
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.
Reposted by Elena Nicolay
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
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
July 10, 2025 at 10:32 AM
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
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
Reposted by Elena Nicolay
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...
These plastic particles smaller than a human hair can pass through cell walls and enter the food web
go.nature.com/44TofaH
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
July 10, 2025 at 10:48 AM
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...
Reposted by Elena Nicolay
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
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
July 8, 2025 at 8:39 AM
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
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
Reposted by Elena Nicolay
Generate beautiful PDF of your manuscripts easily using Markdown. #RxivMaker is here. We hope it will supercharge your #preprints Mojo.
🧑🔬📰🚀 #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...
📜: zenodo.org/records/1575...
👨💻: github.com/HenriquesLab...
June 27, 2025 at 2:08 PM
Generate beautiful PDF of your manuscripts easily using Markdown. #RxivMaker is here. We hope it will supercharge your #preprints Mojo.
Reposted by Elena Nicolay
🔬 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
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
June 25, 2025 at 3:43 PM
🔬 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
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
Reposted by Elena Nicolay
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
#HelmholtzImaging #FAIRdata
June 25, 2025 at 1:26 PM
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
#HelmholtzImaging #FAIRdata
Reposted by Elena Nicolay
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
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
June 18, 2025 at 8:33 AM
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
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
Reposted by Elena Nicolay
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...
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...
June 16, 2025 at 4:49 AM
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...
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...
Reposted by Elena Nicolay
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...
pip install unprompted
github.com/haesleinhuep...
June 15, 2025 at 9:16 AM
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...
pip install unprompted
github.com/haesleinhuep...
Reposted by Elena Nicolay
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
Today’s spotlight: the Helmholtz Information & Data Science platforms – including #HelmholtzImaging, @helmholtzai.bsky.social, HIDA, HIFIS & HMC.
Read more 👇
#Helmholtz #Helmholtz30 #DataScience #imaging
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
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
June 12, 2025 at 9:36 AM
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
Today’s spotlight: the Helmholtz Information & Data Science platforms – including #HelmholtzImaging, @helmholtzai.bsky.social, HIDA, HIFIS & HMC.
Read more 👇
#Helmholtz #Helmholtz30 #DataScience #imaging
Reposted by Elena Nicolay
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/...
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
June 12, 2025 at 6:25 AM
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/...
Dismantling EPA’s research office jeopardizes environmental safety, public health, and US competitiveness | PNAS www.pnas.org/doi/10.1073/...
Reposted by Elena Nicolay
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.
June 5, 2025 at 7:05 AM
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.
Reposted by Elena Nicolay
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.
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...
www.nature.com/articles/s41...
June 3, 2025 at 7:59 PM
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.
Reposted by Elena Nicolay
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...
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
May 16, 2025 at 10:18 AM
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...
Here’s a Jupyter notebook I wrote on how, why & when normalization matters, feedback 💛ly welcome.
👇
haesleinhuepf.github.io/BioImageAnal...
Do you work with large image datasets?
Discover our optimized workflows for efficient metadata annotation and #FAIR data management. 🔬💻
Discover our optimized workflows for efficient metadata annotation and #FAIR data management. 🔬💻
#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...
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...
May 16, 2025 at 7:31 AM
Do you work with large image datasets?
Discover our optimized workflows for efficient metadata annotation and #FAIR data management. 🔬💻
Discover our optimized workflows for efficient metadata annotation and #FAIR data management. 🔬💻
Please take a moment to appreciate the beautiful imaging art that was submitted this year 😍 (also, can you spot my image?)
🎉 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
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
May 12, 2025 at 4:23 PM
Please take a moment to appreciate the beautiful imaging art that was submitted this year 😍 (also, can you spot my image?)
Reposted by Elena Nicolay
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
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...](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:4bzbwekunhj4onto6kjjen7p/bafkreihkk3ofejhwweexwazwi5jpovd2iccgnbzwu6v6n7xiq3oymw4gtq@jpeg)
May 12, 2025 at 3:10 PM
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
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
Reposted by Elena Nicolay
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...
May 12, 2025 at 11:00 AM
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...