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Reposted by Mara Lampert

Peter O'Toole @yorkbioimaging.bsky.social · 25d

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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ScaDS.AI Dresden/Leipzig @scadsai.bsky.social · Sep 12

⭕ 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.👏

👉 https://scads.ai/2nd-general-assembly-2025-in-leipzig/

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Ryan Savill @cryaaa.bsky.social · Sep 12

(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 · Aug 5

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!

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...

focalplane.biologists.com

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Sebi @sebi06.bsky.social · Aug 20

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 · Aug 9

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...

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…

www.sciencedirect.com

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Mara Lampert @marabuuuu.bsky.social · Aug 5

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!

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...

focalplane.biologists.com

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Mara Lampert @marabuuuu.bsky.social · Jul 14

And we are students after all 🤷‍♀️🤣

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Alina Yurenko @alina-yurenko.bsky.social · Jun 23

truly one hour of debugging can save you five minutes of reading documentation

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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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NFDI4BIOIMAGE @nfdi4bioimage.bsky.social · Jun 10

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 · Jun 9

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

Annotating Images in Cellpose - FocalPlane

Annotating Images in Cellpose - How to

focalplane.biologists.com

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Ethan Mollick @emollick.bsky.social · Jun 6

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 · Jun 4

Who does microscopy and has never heard of Bio-Formats? You probably used it anyway

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Anne Carpenter @drannecarpenter.bsky.social · Jun 2

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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Mara Lampert @marabuuuu.bsky.social · Jun 2

For discovering relations between papers "connected papers" and "research rabbits" are tools that I like using. If you want to dive deeper into the content of one specific paper "notebookLM" as already suggested above might help.

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Robert Haase @haesleinhuepf.bsky.social · May 20

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...

Quality assurance of segmentation results - FocalPlane

Quality assurance of segmentation results - Bio-image Analysis with Napari

focalplane.biologists.com

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Robert Haase @haesleinhuepf.bsky.social · May 20

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 · May 16

Glad that it helps, thanks for sharing! 🌻

Mara Lampert @marabuuuu.bsky.social · May 16

Thanks for reading and sharing!😇

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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 9

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 · Apr 28

#NewGroupPicture #BioImageDataScience #BIDS @scadsai.bsky.social @nfdi4bioimage.bsky.social

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FocalPlane @focalplane.bsky.social · Apr 18

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 · Apr 14

Thank you for this very versatile dataset @alisterburt.bsky.social. Like it a lot!