Mara Lampert
@marabuuuu.bsky.social
Communicative mind between biology and computer science. http://scads.ai / uni leipzig
CMS master student tu dresden #bioimageanalysis
👩💻 https://github.com/marabuuu
✏️ https://focalplane.biologists.com/author/marabuuu/
CMS master student tu dresden #bioimageanalysis
👩💻 https://github.com/marabuuu
✏️ https://focalplane.biologists.com/author/marabuuu/
Pinned
Mara Lampert
@marabuuuu.bsky.social
· Aug 5
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
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!
Reposted by Mara Lampert
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.
👉 https://f.mtr.cool/ajbildzipj
#SmartPrompts
👉 https://f.mtr.cool/ajbildzipj
#SmartPrompts
November 5, 2025 at 12:03 PM
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.
👉 https://f.mtr.cool/ajbildzipj
#SmartPrompts
👉 https://f.mtr.cool/ajbildzipj
#SmartPrompts
Reposted by Mara Lampert
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...
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...
October 1, 2025 at 1:06 PM
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...
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...
Reposted by Mara Lampert
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
Reposted by Mara Lampert
⭕ 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/
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/
September 12, 2025 at 7:02 AM
⭕ 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/
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/
Reposted by Mara Lampert
(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...
September 12, 2025 at 12:44 PM
(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...
Reposted by Mara Lampert
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
August 5, 2025 at 3:13 PM
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!
Reposted by Mara Lampert
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...
- open complete CZI images or subsets
- read CZI metadata
pypi.org/project/napa...
or
github.com/sebi06/napar...
August 20, 2025 at 6:23 PM
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...
- open complete CZI images or subsets
- read CZI metadata
pypi.org/project/napa...
or
github.com/sebi06/napar...
Reposted by Mara Lampert
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
August 9, 2025 at 8:39 AM
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...
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
August 5, 2025 at 3:13 PM
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!
Reposted by Mara Lampert
truly one hour of debugging can save you five minutes of reading documentation
June 23, 2025 at 1:21 PM
truly one hour of debugging can save you five minutes of reading documentation
Reposted by Mara Lampert
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 Mara Lampert
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...
Find the poster here:
👉 zenodo.org/records/1483...
June 10, 2025 at 1:32 PM
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...
Find the poster here:
👉 zenodo.org/records/1483...
Reposted by Mara Lampert
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
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
June 9, 2025 at 9:43 AM
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
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
Reposted by Mara Lampert
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...
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...
June 6, 2025 at 4:14 PM
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...
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...
Reposted by Mara Lampert
Who does microscopy and has never heard of Bio-Formats? You probably used it anyway
June 4, 2025 at 9:13 PM
Who does microscopy and has never heard of Bio-Formats? You probably used it anyway
Reposted by Mara Lampert
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?
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?
June 2, 2025 at 10:27 AM
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?
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?
Reposted by Mara Lampert
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
May 20, 2025 at 10:29 AM
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...
Reposted by Mara Lampert
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...
I just added a Notebook demonstrating how to do this to the #BioImageAnalysisNotebooks 🔬🖥️📈
haesleinhuepf.github.io/BioImageAnal...
May 20, 2025 at 7:35 AM
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...
I just added a Notebook demonstrating how to do this to the #BioImageAnalysisNotebooks 🔬🖥️📈
haesleinhuepf.github.io/BioImageAnal...
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...
Reposted by Mara Lampert
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.
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.
May 9, 2025 at 4:28 PM
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.
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.
Reposted by Mara Lampert
Reposted by Mara Lampert
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
Let us know if we are missing any recent preprints that you enjoyed.
#bioimageanalysis #datamanagement
focalplane.biologists.com
April 18, 2025 at 9:01 AM
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
Let us know if we are missing any recent preprints that you enjoyed.
#bioimageanalysis #datamanagement
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!
April 14, 2025 at 11:48 AM
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!
Reposted by Mara Lampert
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! 🚀
Do you want to use LLMs in applications in science or industry?
Join us for this two-day training in Leipzig! 🚀
We are pleased to announce our #LLMs in Science & Industry Training on May 12-13, 2025! 🌻
Gain insights into LLMs, the fundamentals of #DeepLearning, fine-tuning & ethical considerations of LLMs. Ideal for researchers, engineers and industry professionals.
👉 Registration: pretix.eu/infai/scadsa...
Gain insights into LLMs, the fundamentals of #DeepLearning, fine-tuning & ethical considerations of LLMs. Ideal for researchers, engineers and industry professionals.
👉 Registration: pretix.eu/infai/scadsa...
April 10, 2025 at 4:13 PM
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! 🚀
Do you want to use LLMs in applications in science or industry?
Join us for this two-day training in Leipzig! 🚀
Reposted by Mara Lampert
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/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
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...
journals.biologists.com
April 7, 2025 at 9:15 AM
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/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