Wei-Chen CHU
LightNews LightNews
weichen01.bsky.social
Wei-Chen CHU
@weichen01.bsky.social
300 followers 700 following 7 posts
R&D Scientist@ICOB Imaging Core, Academia Sinica, Taiwan
https://weichenchu.com/
https://eabias.github.io/
https://www.linkedin.com/in/weichen-chu/
https://orcid.org/0000-0002-3447-9043
Posts Replies Media Videos
Pinned
weichen01.bsky.social
Wei-Chen CHU @weichen01.bsky.social · May 10
📣 The EABIAS "ImageJ Microscopic Image Analysis & Macro Programming" course has wrapped up!

🔓 All resources now freely available under CC-BY license:
Slides in English/ Recordings in Mandarin Chinese

🔗 github.com/EABIAS/2025-...

#ImageJ #Fiji #BioImaging #OpenScience #EABIAS
GitHub - EABIAS/2025-ImageJ-Micro-Image-Analysis-and-Programming_Taipei
Contribute to EABIAS/2025-ImageJ-Micro-Image-Analysis-and-Programming_Taipei development by creating an account on GitHub.
github.com
Reposted by Wei-Chen CHU
dstansby.bsky.social
Today I'm announcing a new digital textbook 📖🖥️, "An Introduction to OME-Zarr for Big Bioimaging Data".

ome-zarr-book.readthedocs.io
An Introduction to OME-Zarr for Big Bioimaging Data
ome-zarr-book.readthedocs.io
November 4, 2025 at 3:33 PM
Reposted by Wei-Chen CHU
haesleinhuepf.bsky.social
I just finished my @unileipzig.bsky.social #LunchLecture. Thanks everyone for the vivid discussion and Nicole Koburger for hosting us!
The slides are online #openaccess 🧑‍🏫🔓 zenodo.org/records/1742...
October 23, 2025 at 11:19 AM
Reposted by Wei-Chen CHU
jytinevez.bsky.social
Save the date! The @pasteur.fr Pasteur course on image analysis is announced:

It will happen from the 1st of June to the 5th 2026.

This year there will be only one track: the Early Career Investigator track (beginners). 👇
September 10, 2025 at 12:50 PM
Reposted by Wei-Chen CHU
yorkbioimaging.bsky.social
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
September 19, 2025 at 11:15 AM
Reposted by Wei-Chen CHU
focalplane.bsky.social
📢Last few days to apply for this round of our #microscopy training grants with @jcellsci.bsky.social

Available to ECRs working on #cellbio to attend a microscopy or bioimage analysis training course.

Apply by 5 September

www.biologists.com/grants/jcs-f...
Microscopy Training Grants Supporting microscopy training for early-career researchers in cell biology Apply for a grant of up to £1,000 Cartoon of a person looking down a microscope, which is next to a computer Journal of Cell Science logo and FocalPlane logo
August 29, 2025 at 1:14 PM
Reposted by Wei-Chen CHU
dudinlab.bsky.social
A new #UExM probe for #Actin!

Fun times thinking/developing/testing with @centriolelab.bsky.social & @lreymond.bsky.social !

Congrats to all !

If interested in #UExM, or #HAK-Actin, feel free to reach out !

Soon available at @spirochrome.com

#Expansion #Microscopy #ProtistsOnSky
centriolelab.bsky.social Paul & Virginie - Centriole Lab @centriolelab.bsky.social · Aug 28
Trouble imaging actin in ExM? Meet HAK-Actin, a probe for U-ExM, cryo-ExM & iU-ExM. Enables post-expansion labeling for max signal. www.biorxiv.org/content/10.1...
Soon at @spirochrome.com
Led by O.Mercey and @lreymond.bsky.social, in collab with @dudinlab.bsky.social and @marinelap.bsky.social
August 28, 2025 at 7:16 AM
Reposted by Wei-Chen CHU
gideproject.bsky.social
The #foundingGIDE Community Event 2025 program is now live!

📌 Location: Brisbane, Australia & Online
📅 Deadline: 31st August
📃 Program: docs.google.com/document/d/1...

@globalbioimaging.bsky.social @nifaustralia.bsky.social @micro-au.bsky.social @eurobioimaging.bsky.social

#imaging #bioimaging
August 25, 2025 at 12:19 PM
Reposted by Wei-Chen CHU
sebi06.bsky.social
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...
August 20, 2025 at 6:23 PM
Reposted by Wei-Chen CHU
nfdi4bioimage.bsky.social
Interested in #bioimaging and #datascience? The "Bio-Image Data Science Lectures 2025 @unileipzig.bsky.social / @scadsai.bsky.social" by @haesleinhuepf.bsky.social offer theory and practice on #Python, #machinelearning, #deeplearning, #LLMs, and research data.

📝 zenodo.org/records/1585...
August 14, 2025 at 12:54 PM
Reposted by Wei-Chen CHU
indiabioimaging.bsky.social
Launching the #IBIWebinarSeries!

Join us for the talk by Prof. Sudipta Maiti, Senior Professor, Dept of Biological Sciences, BITS, Pilani, Hyderabad Campus

Title: “Light Microscopy: The Newest Kids on the Block”
Time: July 25, 2025 | 3–4 PM IST

Register here: uu-se.zoom.us/webinar/regi...
July 18, 2025 at 7:27 AM
Reposted by Wei-Chen CHU
fabmusacchio.bsky.social
✍️ New in #eLife: #CellSeg3D introduces #WNet3D, a self-supervised 3D #segmentation method for #microscopy data — no labels needed. Claims to outperform #Cellpose/#StarDist on 4 datasets. Includes #opensource plugin (#Napari) + full 3D annotated #cortex dataset. Will test it later.
@napari.org
July 11, 2025 at 1:58 PM
Reposted by Wei-Chen CHU
haesleinhuepf.bsky.social
It was an honor to give a keynote lecture about #VLMs for Bio-Image #DataScience at the @helmholtzimaging.bsky.social #HIconference2025.
You find my slides #openaccess 🔬🖥️🚀
doi.org/10.5281/zeno...
June 25, 2025 at 5:19 PM
Reposted by Wei-Chen CHU
haesleinhuepf.bsky.social
I just finished a full-day hands-on tutorial about applications of LLMs as part of the @scadsai.bsky.social Summer School. Big thanks everyone for the lively discussions about prompt engineering, code&data generation, RAG, vision, function calling and #AI agents 🖥🤖🚀
scads.github.io/LLM_Summer_S...
ScaDS.AI Summer School LLM Training This is a collection of Jupyter Notebooks about basic and advanced LLM usage, focusing on what’s practicslly possible with Large Language Models. We demonstrate most utilities using the ScaDS.AI Large Language Models (LLM) Servicer (TU Dresden VPN required). Most exercises should also work with other providers such as GWDG KISSKI and Helmholtz Blablador. The tutorial aims at Python programmers who want to dive into LLMs for generating text, code and data using open source/weights models. After this course they will be able to integrate LLMs into their software applications. Contributions and feedback are very welcome! In case you see room for improvement, please create a github issue and/or consider contributing. Topics The notebook collection aims covering these topics: Large Language Models (LLMs) Text/Code/Data generation Prompt Engineering Retrieval-augmented-generation Vision Function calling Agents Covered Python libraries and software In these notebooks we use libraries from the GenAI field: bia-bob llama-index ollama openai Slide decks Also training slides can be downloaded from zenodo: https://doi.org/10.5281/zenodo.15743126 Videos The materials provided here were also discussed in a couple of recorded Online Lectures Large Language Models for Bio-image Analysis (ScaDS.AI Living Lab lecture 2024) Large Language Models – an introduction for life scientists (GloBIAS Seminar 2024) Bio-image Analysis Code Generation (I2K Conference 2024) Generative Artificial Intelligence for Bio-image Analysis Related resources The notebooks presented here were partially taken from other places or inspired by code in these resources:
June 26, 2025 at 5:03 PM
Reposted by Wei-Chen CHU
gerbi-gmb.de
Core facility contributions are essential, and #ImagingScientists deserve to receive #CreditWhereItsDue. That’s why we fully support the #AcknowledgementGuidelines launched by @royalmicrosoc.bsky.social and @globalbioimaging.bsky.social and have proudly displayed them in our digital office.
June 23, 2025 at 1:52 PM
Reposted by Wei-Chen CHU
biaunit.bsky.social
🚀 Manual mask annotation slowing you down?
💡 SAMJ is a new ImageJ/Fiji plugin using Segment Anything (SAM) for fast, interactive segmentation — no GPU needed, one-click install, real-time results.
🔬 Perfect for large biomedical images.
arxiv.org/abs/2506.02783
#AI #Bioimaging #ImageJ #OpenSource
June 17, 2025 at 8:16 AM
Reposted by Wei-Chen CHU
haesleinhuepf.bsky.social
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...
June 15, 2025 at 9:16 AM
Reposted by Wei-Chen CHU
nkiaru.bsky.social
Why #BigDataViewer loves multi-resolution (pyramidal) formats:
- Top left: Only high-res data → slow & artifacts when zoomed out.
- Top right: Only low-res data → no details when zoomed in.
- Bottom: All resolutions → seamless, responsive, beautiful. 🎥

#FijiSc
November 27, 2024 at 10:21 AM
Reposted by Wei-Chen CHU
hms-iac.bsky.social
🎀✨Recording now available ✨🎀

youtu.be/jtDunWK8g1o?...
June 6, 2025 at 3:14 PM
Reposted by Wei-Chen CHU
focalplane.bsky.social
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
June 9, 2025 at 9:43 AM
Reposted by Wei-Chen CHU
jytinevez.bsky.social
Our paper describing the creation of a nationwide core facility for bioimage analysis if out in @plos Computational Biology!
🎉✌️

journals.plos.org/ploscompbiol...

So happy about this paper and how the work turned out.
A small thread 👇

#bioimageanalysis #corefacility
F-BIAS: Towards a distributed national core facility for bioimage analysis †
Author summary We describe our experience in creating a nationwide core facility offering services in bioimage analysis. This virtual facility federates existing resources scattered across the territo...
journals.plos.org
June 11, 2025 at 8:29 AM
Reposted by Wei-Chen CHU
haesleinhuepf.bsky.social
#biabob 0.28.0 is out and it comes with support for OpenAI's codex-mini model. I also enabled its vision-support. With this, you can turn screenshots of user-interfaces into functional code - directly within your Jupyter notebook 🤯
github.com/haesleinhuep...
June 1, 2025 at 10:57 AM
Reposted by Wei-Chen CHU
natmethods.nature.com
A universal AI-powered pipeline enables precise 3D analysis of cell morphology and topology within organoid structures.

www.nature.com/articles/s41...
May 14, 2025 at 4:17 PM
Reposted by Wei-Chen CHU
haesleinhuepf.bsky.social
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...
May 20, 2025 at 7:35 AM
Reposted by Wei-Chen CHU
globias.bsky.social
Next #GloBIAS seminar coming up. Curtis Rueden will present on 'Fiji with Python power'. To get the link please register here: www.globias.org/activities/b...
May 19, 2025 at 4:23 PM
Reposted by Wei-Chen CHU
marabuuuu.bsky.social
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
May 16, 2025 at 10:18 AM