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Mara Lampert

@marabuuuu.bsky.social
186 followers 305 following 12 posts

Communicative mind between biology and computer science. scads.ai / uni leipzig CMS master student tu dresden #bioimageanalysis 👩‍💻 github.com/marabuuu ✏️ focalplane.biologists.com/author/ma…

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Reposted by Mara Lampert
Martin Weigert @maweigert.bsky.social · 02/03/2026
Excited to share our new paper (CVPR 2026 🚀): "MuViT: Multi-Resolution Vision Transformers for Learning Across Scales in Microscopy" which enables local predictions to use global context. Great work led by @albertdm.bsky.social & another fun collab w @gioelelamanno.bsky.social! @scadsai.bsky.social
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Mara Lampert @marabuuuu.bsky.social · 19/02/2026
Super grateful that the @ymia.gerbi-gmb.de and especially @enicolay.bsky.social helped me to bring the vision of this panel discussion to life. 🚀⭐ It was an incredible experience to moderate this event. I truly hope that this panel discussion gives some new & different insights. Enjoy listening! 1/3
youtube.com
The Power of Sharing: Open Data in Bio-image Analysis
YouTube video by Young Microscopists and Image Analysts
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Young Microscopists and Image Analysts @ymia.gerbi-gmb.de · 01/01/2026
Happy New Year YMIA! Another full year has come to an end: we hosted microscopy watchparties, joined key imaging conferences & organized a panel on Open Data in Bioimage Analysis (available soon on YouTube) In 2026, expect invited talks on practical image analysis & more opportunities to connect🍀🥂🔬🎉
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ScaDS.AI Dresden/Leipzig @scadsai.bsky.social · 05/11/2025
Lea Kabjesz, Lea Gihlein, @marabuuuu.bsky.social and Luisa Götze led a workshop at @scadsai.bsky.social General Assembly, titled “Coding Effectively with AI: Getting Started with Cursor and Copilot”. The slides are free and suitable for beginners. 👉 f.mtr.cool/ajbildzipj #SmartPrompts
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NFDI4BIOIMAGE @nfdi4bioimage.bsky.social · 01/10/2025
Save the date for the panel discussion “The Power of Sharing: Open Data in Bioimage Analysis” on October 24, 2025. 🤝 The discussion with experts from various fields related to imaging is organized by Young Microscopists and Image Analysts (YMIA). Register here: 👉 gerbi-gmb.de/machform/vie...
Poster for the panel discussion: The Power of Sharing: Open Data in Bio-image Analysis on October 24, 2025 starting 1:30 pm on site at the KUBUS Hall 1A, UFZ Leipzig or online starting at 2:00 pm. In the lower part of the poster the experts are listed with pictures and names, as well as the moderation.
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Peter O'Toole @yorkbioimaging.bsky.social · 19/09/2025
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
bit.ly
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...
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ScaDS.AI Dresden/Leipzig @scadsai.bsky.social · 12/09/2025
⭕ This week at @scadsai.bsky.social : We held the 2nd General Assembly in 2025 in Leipzig. The program included talks, workshops, and a poster session. We awarded the "Best PhD Poster Award" to Lea Gihlein, Lea Kabjesz, and Maja Schneider.👏 👉 scads.ai/2nd-general-assembly-2025-…
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Ryan Savill @cryaaa.bsky.social · 12/09/2025
(1/14) I’m happy and proud to introduce: SpinePy – a framework to detect the "spine" of gastruloids and measure biological and physical signals in a local dynamic 3D coordinate system. www.biorxiv.org/content/10.1...
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Mara Lampert @marabuuuu.bsky.social · 05/08/2025
Ensuring reproducibility in GUI-based bio-image analysis tools can be tricky, so I wrote this new blog post on @focalplane.bsky.social. It highlights features in Napari, Fiji, QuPath, Galaxy, CellProfiler and JIPipe that support workflow saving and sharing. Hope it helps! 🤗🔬👩‍💻Feedback 💛ly welcome!
focalplane.biologists.com
From Click to Code: Reproducible Bio-image Analysis
Graphical user interfaces (GUIs) make image analysis more intuitive and accessible, but they also come with a hidden risk: the steps we take aren’t always fully documented or easy to reproduce. To mak...
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Sebi @sebi06.bsky.social · 20/08/2025
I finally managed to upload the first version of the napari-czitools plugin (still in alpha - expect issues...) - open complete CZI images or subsets - read CZI metadata pypi.org/project/napa... or github.com/sebi06/napar...
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Rita Mateus @ritamateus.bsky.social · 09/08/2025
Hot off the press!!! Proudly presenting our lab's new review on how do cells communicate to control organ size :) We focus specially on dynamic connections that operate at different timescales to regulate organ growth and morphogenesis. #devbio #SizeandShape www.sciencedirect.com/science/arti...
sciencedirect.com
Start-Shape-Stop: Cell communication mechanisms controlling organ size
Accurate growth control is critical for the achievement of proportional organs during animal development and repair processes. Either extra or deficie…
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Mara Lampert @marabuuuu.bsky.social · 05/08/2025
Ensuring reproducibility in GUI-based bio-image analysis tools can be tricky, so I wrote this new blog post on @focalplane.bsky.social. It highlights features in Napari, Fiji, QuPath, Galaxy, CellProfiler and JIPipe that support workflow saving and sharing. Hope it helps! 🤗🔬👩‍💻Feedback 💛ly welcome!
focalplane.biologists.com
From Click to Code: Reproducible Bio-image Analysis
Graphical user interfaces (GUIs) make image analysis more intuitive and accessible, but they also come with a hidden risk: the steps we take aren’t always fully documented or easy to reproduce. To mak...
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Alina Yurenko @alina-yurenko.bsky.social · 23/06/2025
truly one hour of debugging can save you five minutes of reading documentation
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Robert Haase @haesleinhuepf.bsky.social · 15/06/2025
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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NFDI4BIOIMAGE @nfdi4bioimage.bsky.social · 10/06/2025
Michele Bortolomeazzi, Christian Schmidt and Jan-Philipp Mallm at @nfdi4bioimage.bsky.social have developed a new OMERO-web plugin: OMERO-vitessce. It enables the visualization of datasets hosted in #OMERO with the #Vitessce multimodal data viewer. Find the poster here: 👉 zenodo.org/records/1483...
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FocalPlane @focalplane.bsky.social · 09/06/2025
New ‘How to’ post on FocalPlane 🔬💻 Lea Kabjesz shares a step-by-step guide to get you started annotating 2D and 3D images in Cellpose, including video tutorials. focalplane.biologists.com/2025/06/05/a... #bioimageanalysis #cellpose #imaging #HowTo
focalplane.biologists.com
Annotating Images in Cellpose - FocalPlane
Annotating Images in Cellpose - How to
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Ethan Mollick @emollick.bsky.social · 06/06/2025
Example of why I think current LLMs are enough to change lots of work even if they don’t get better, once we start integrating them with other systems GPT-4 (now obsolete) went from 30% accuracy to 87% accuracy in clinical oncology decisions when given access to tools www.nature.com/articles/s43...
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Tom Boissonnet @tom-bssnnt.bsky.social · 04/06/2025
Who does microscopy and has never heard of Bio-Formats? You probably used it anyway
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Anne Carpenter @drannecarpenter.bsky.social · 02/06/2025
Help! Let’s say I have 200 scientific papers in my digital to-read pile I could stay in denial, or I could ask AI for help. Any workflows/tools to group them in some meaningful way? This alone would help mental load as I at least read abstracts And/or any good summary tools?
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Robert Haase @haesleinhuepf.bsky.social · 20/05/2025
I regularly point collaborators at this segmentation quality assurance blog post by @marabuuuu.bsky.social , because some scientists get trapped in a segmentation-improvement-loop without ever measuring how good an algorithm actually is. focalplane.biologists.com/2023/04/13/q...
focalplane.biologists.com
Quality assurance of segmentation results - FocalPlane
Quality assurance of segmentation results - Bio-image Analysis with Napari
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Robert Haase @haesleinhuepf.bsky.social · 20/05/2025
If you use ML for pixel classification, e.g. using sckit-learn, you can use SHAP analysis for explaining how relevant the feature images are you provided. I just added a Notebook demonstrating how to do this to the #BioImageAnalysisNotebooks 🔬🖥️📈 haesleinhuepf.github.io/BioImageAnal...
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Mara Lampert @marabuuuu.bsky.social · 16/05/2025
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...
haesleinhuepf.github.io
Image Normalization — Bio-image Analysis Notebooks
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Elena Nicolay @enicolay.bsky.social · 09/05/2025
The YMIA would like to invite everyone interested in microscopy and image analysis to our weekly watch-parties. This Tuesday we cover how to choose the right microscope for your experiment as well as learning how to minimize damage to samples during light microscopy.
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Robert Haase @haesleinhuepf.bsky.social · 28/04/2025
#NewGroupPicture #BioImageDataScience #BIDS @scadsai.bsky.social @nfdi4bioimage.bsky.social
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FocalPlane @focalplane.bsky.social · 18/04/2025
In this week’s preprint list, we focus on the latest research in bioimage analysis and data management. Let us know if we are missing any recent preprints that you enjoyed. #bioimageanalysis #datamanagement
focalplane.biologists.com
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Mara Lampert @marabuuuu.bsky.social · 14/04/2025
Hi everyone! I am searching for a CC-BY 4.0 licensed biological dataset (ideally images but do not have to be) for feature exploration and data visualisation. Ideally, it should be between 100KB and 1GB. Inspiration 💛ly welcome!
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Robert Haase @haesleinhuepf.bsky.social · 10/04/2025
Do you want to understand better how LLMs work? Do you want to use LLMs in applications in science or industry? Join us for this two-day training in Leipzig! 🚀
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Guillaume Jacquemet @guijacquemet.bsky.social · 07/04/2025
Here we share our opinions on "Practical considerations for data exploration in quantitative cell biology" journals.biologists.com/jcs/article/... Joanna, Hanna and I worked quite a bit on this piece and I hope you find it useful Many thanks to @jcellsci.bsky.social for publishing it
journals.biologists.com
Practical considerations for data exploration in quantitative cell biology
Summary: We present practical guidelines for data exploration in quantitative cell biology that are designed to help yield reliable conclusions and promote a collaborative, transparent approach to dat...
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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 08/04/2025
Bioimaging and bioimage analysis friends, some help if you have 2-3 mins; for a paper, we're trying to estimate the number of biologists trained in open source software or tools in the last ~5 years. (1/2) #bioimaging #microscopy #bioimageanalysis
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Robert Haase @haesleinhuepf.bsky.social · 27/03/2025
The #gitbob paper has been published in @natcomputsci.bsky.social.🥳 Learn about the path "Towards transparency and knowledge exchange in AI-assisted data analysis code generation" facilitating how humans and AI can work together to solve #dataanalysis tasks. 💽🧑‍🎓🖥️🏗️ rdcu.be/efkna
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eurobioimaging.bsky.social @eurobioimaging.bsky.social · 20/02/2025
Are you a student 🧑‍🎓 , group leader 🧑‍🔬 , data manager or imaging facility staff🔬 interested in #imagedata? Join the #EuroBioImaging Image Data Community Days, a FREE, online event taking place from 🗓️ April 7-11 to explore advancements in the field of image data. More 🔽 buff.ly/3CHd9uf
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ScaDS.AI Dresden/Leipzig @scadsai.bsky.social · 05/02/2025
The people behind the project globias.bsky.social share a common vision: To bring together data scientists working in microscopy and share their knowledge. scadsai.bsky.social researcher haesleinhuepf.bsky.social and his colleagues about the idea of the project: 👉 www.youtube.com/watch?v=LPJE...
youtube.com
GloBIAS: Global BioImage Analysts' society - the idea
YouTube video by GloBIAS
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Henning Falk Illustrations @falk-illustrations.de · 22/01/2025
A cartoon I drew a while ago for @gerbi-gmb.de to illustrate the power of research data management in science. Who knows where #RDM and data sharing might lead us to? If even ostriches can fly... 🚀🐥
This is a black-and-white cartoon. On the left side are 3 ostriches, each with their head in their own pile of sand. The pile of sands are labelled with "my data". There is an arrow which points to the right side, labelled RDM (research data management). On the right side are 2 ostriches with their head in one huge cloud, labelled "our data". The third ostrich is flying away.
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Robert Haase @haesleinhuepf.bsky.social · 21/01/2025
I recently visited TU Dresden for two guest lectures about Prompt Engineering, RAG, Agents and Multi-Modal #LLMs. thanks to Simon Razniewski @scadsai.bsky.social for having me! My slides are available #openaccess 💻🤖🔓 zenodo.org/records/1469...
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ScaDS.AI Dresden/Leipzig @scadsai.bsky.social · 20/01/2025
As #ScaDS.AI, we're excited to share our research on scalable #datascience and #AI on Bluesky from now on. 🦋 With our two locations, Leipzig University and tudresden.bsky.social, we combine excellent AI, data science and big data expertise. 👉 Follow us: @scadsai.bsky.social
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Henning Falk Illustrations @falk-illustrations.de · 13/01/2025
I’m so excited to share my new website with you all! 🎉 Check it out at falk-illustrations.de, explore my artwork, and feel free to reach out if you're interested in commissions or just want to chat! #SciArt #Illustration #NewWebsite #Cartoons #Excited #AndABitProud
falk-illustrations.de
Home
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Mattan S. Ben-Shachar @mattansb.msbstats.info · 06/01/2025
Hey #StatsSky, what are you favorite papers to cite when you need to justify something that is obvious (I once had a reviewer ask we justify the use of logistic regression on a binary outcome) or when you need to push-back on silly reviewer requests (e.g., asking for p-values in table 1)?
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Inês Cunha @inesmcunha.bsky.social · 02/01/2025
And to start 2025 strong… Our work #NanoPyx is out in Nature Methods 😍❤️ DOI: doi.org/10.1038/s415... #NanoPyx is a Python framework that uses the #LiquidEngine to efficiently accelerate bioimage analysis for any user! (1/n) ⬇️
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Journal of Cell Science @jcellsci.bsky.social · 20/12/2024
In her Essay, Julie Welburn @jwelburn.bsky.social highlights the environmental impact of biomedical research and shares ten easy tips to help reduce your lab’s carbon footprint. journals.biologists.com/jcs/article/...
journals.biologists.com
How to reduce your lab's carbon footprint
Although we are all dedicated to conducting high-quality, cutting-edge research in the basic and applied biomedical sciences, it is important to acknowledge the environmental impact of our work. The b...
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Robert Haase @haesleinhuepf.bsky.social · 18/12/2024
A little #milestone for the #biabob project: 💯 Github Stars ⭐⭐⭐ 🚀 I'm happy to see the growing community using #biabob as #BioImageAnalysis Coding Assistant in Jupyter. I would love to learn more about what people use it for! Feel free to share screenshots below 😃 github.com/haesleinhuep...
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Robert Haase @haesleinhuepf.bsky.social · 13/12/2024
Jeey! @nfdi4bioimage.bsky.social published their #RDM-related postcards FAIRly (made by Henning Falk, licensed CC-BY 4.0) 🔬💾😍 github.com/NFDI4BIOIMAG...
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Kai Kupferschmidt @kakape.bsky.social · 06/12/2024
If an #H5N1 pandemic starts tomorrow or in three months, there will be little mystery as to how it happened. The conditions are all there. They have been for a while. So in some ways the more interesting question to me at the moment is: Why aren’t we in a pandemic yet? Story here, 🧵 to come: 🧪#IDSky
science.org
Why hasn’t the bird flu pandemic started?
Some scientists examining mutations found in H5N1 viruses fear major outbreak is imminent but others says pathogen remains unpredictable
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Kara Cerveny @kara-cerveny.bsky.social · 06/12/2024
My go to for color ideas: thenode.biologists.com/data-visuali... Personally like green, magenta, and orange for microscopy; each channel in grey and then a merged colorized image also recommended.
thenode.biologists.com
Color blind friendly palettes for data visualizations with categories
A discussion of color blind friendly palettes for labeling unique catergories in data visualization.
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Robert Aboukhalil @robert.bio · 04/12/2024
“We don’t value software, data, and methods in the same way we value papers, even though those resources empower millions of scientists” 💯 www.statnews.com/sponsor/2024...
statnews.com
New report highlights the scientific impact of open source software
Two of the scientists who won this year’s Nobel Prize for cracking the code of proteins’ intricate structures relied, in part, on a series of computing
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The Company of Biologists @biologists.bsky.social · 03/12/2024
🧪 Guess the image quiz starts today - Take #ACloserLook 🔎 🎵I see blobs of blue Red circles too I see them move For me and you And I think to myself What could this image be?
A close-up of blue spheres with red circles inside.
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Tomer Ullman @tomerullman.bsky.social · 01/12/2024
thinking of calling this "The Illusion Illusion" (more examples below)
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Alexandre @alexandredizeux.bsky.social · 26/11/2024
Here are two covers proposals for the current Cell issue, but it didn't make it. I love these renders because they are just data, nothing else! Congrats to @merlinlange.bsky.social & @loicaroyer.bsky.social ! #dataviz #sciart 🐡 🧪 Data imported and rendered in #houdini @sidefx.bsky.social
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FocalPlane @focalplane.bsky.social · 29/11/2024
Our preprint list is now up on FocalPlane. This week we focus on research in #bioimageanalysis. Drop us a message if we’re missing any preprints that you’ve been reading or writing! focalplane.biologists.com/2024/11/29/m...
focalplane.biologists.com
Microscopy preprints - bioimage analysis - FocalPlane
Microscopy preprints - bioimage analysis - Discussions
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Robert Haase @haesleinhuepf.bsky.social · 01/12/2024
Voilà! #gitbob and #biabob were updated to support #pixtral, the vision model from the French mistral.ai #LLM provider. It also comes with a free tier 🇫🇷 🇪🇺 🎉 github.com/haesleinhuep... github.com/haesleinhuep...
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Karsten Roth @confusezius.bsky.social · 28/11/2024
🤔 Can you turn your vision-language model from a great zero-shot model into a great-at-any-shot generalist? Turns out you can, and here is how: arxiv.org/abs/2411.15099 Really excited to this work on multimodal pretraining for my first bluesky entry! 🧵 A short and hopefully informative thread:
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