Marco Dalla Vecchia

GloBIAS: strengthening the foundations of BioImage Analysis There is a global need for BioImage Analysis (BIA) as advances in life sciences increasingly rely on cutting-edge imaging systems that have dramatically expanded the complexity and dimensionality of b...

@kbias.bsky.social, @pmsampaio.bsky.social, @tischi.bsky.social, Rocco D'Antuono, ‪and @haesleinhuepf.bsky.social
‬ did a great job of pulling the data together, to describe who we are, where we want to get, and how we get there together. Check out the preprint and join us today! (5/5)

We had a case in the past in which segmentation on brightfield images was near impossible and having fluorescence made it straightforward. We then had another user coming with brightfield only data, and being able to predict fluorescence signal from this new data for segmentation would have saved us

From the screenshot, these spots are extremely well defined and easy to detect with any DoG or LoG methods. I would do this in Fiji but you could give it a try to SpotMAX

In our user base, we experienced several times corrupted files for no apparent reasons. We tried to boil it down to machine, data storage location, loss of connection but nothing seems to relate. A curiosity which Jmaris version are you working with? Most of our corruptions happened with v9

Very cool :)

Napari 3D view screenshot depicting a labeled bacteria dataset

And here's the full labeling by one of our users for the full training patch. Some errors to still correct, but such a time saver!

We've been trying nnInteractive (github.com/MIC-DKFZ/nap...) to quickly create labeled data for later training an Omnipose model. I whatever black magic you did there, keep at it! It's such a life-changer!

Any scikit-image fans in Vienna? The skimage team would like to meet in Vienna for a code sprint Aug 14-16 ahead of EuroSciPy. We'd super appreciate it if someone's workplace can host us! All we need is electricity, natural light, and (most important) walking distance to coffee. ☕️😂🙏

We've already inquired unfortunately it's not so easy to accommodate completely external events..

🌍 GloBIAS is now open for members!
Join our global community of scientists, developers & microscopists advancing BioImage Analysis.
Let’s build tools, share knowledge & shape the field together.
🔗 More information: tinyurl.com/mtvjadex
#BioImageAnalysis #GloBIAS #OpenScience

I'll admit I was not 100% sure the filename was a joke! 😅😅

If a community of software developers struggles with version control of their own documents, I don't think I have a chance 👀 look at that file name 😅

GitHub - carpentries-incubator/bioimage-analysis-python: Bioimage Analysis with Python Bioimage Analysis with Python. Contribute to carpentries-incubator/bioimage-analysis-python development by creating an account on GitHub.

Final outcome? We already have a new lesson in the Data Carpentry incubator that hopefully will become the end-product curriculum stemmed from this workshop: github.com/carpentries-...

Make sure to follow this work and reach out if you want to contribute!

We had many more @globias.bsky.social members and volunteers who joined the initiative and provided key contributions to the discussion and development of the new curriculum! We hope to many of you actively contributing to the actual content very soon!

Full room following Robert Haase lecture on the background

Robert Haase presenting his slides on "Learning and Training #BioImageAnalysis in the Age of AI"

We also invited @haesleinhuepf.bsky.social who gave us an excellent and super relevant talk about "Learning and Training #BioImageAnalysis in the Age of AI".

His experience in image analysis and teaching gave further push to the initiative with concrete solutions. Thank you for joining!

We also had the crucial presence of lesson and curriculum advisors @k-meech.bsky.social and Marianne Corvellec presenting the history and goals of the current image processing curriculum (github.com/datacarpentr...). They were also essential in guiding the conversation and subgroups! Thank you both!

Toby Hodges Director of Curriculum of the Carpentries presenting the organization

During the event, we had the honor of having the Director of Curriculum @tobyhodges.bsky.social himself giving us an intro to @carpentries.carpentries.org philosophy and goals.

He provided essential wisdom and guidance in steering the discussion for the course approach and content. Thank you, Toby!

GloBIAS and Data Carpentry members group picture

In the past 2 days, we had the great pleasure to host an in-person workshop at @istaresearch.bsky.social with the collaboration of @globias.bsky.social, @carpentries.carpentries.org and @istaustria-iof.bsky.social.

We wanted to create a go-to course for image analysis in Python. Info in the thread!

Open Source Bioimage Analysis Training Survey We are attempting for a publication to estimate the number of biologists who have attended a tutorial or training course in open source bioimage analysis (especially user friendly tools, but anything ...

If you train people in ImageJ, Fiji, whatever, even if it isn't your day job, please let us know, and please share this post! Thanks a ton, we really appreciate it. (2/2) forms.gle/C8dUpg8qZkbD... #bioimaging #microscopy #bioimageanalysis

Very happy to have the @globias.bsky.social & @carpentries.carpentries.org workshop at @istaresearch.bsky.social with key contributions of @Tereza Belinova, @marcodv.bsky.social and @sommerinvienna.bsky.social from our @istaustria-iof.bsky.social faculty team

Hey @jytinevez.bsky.social! This program looks fantastic! Do you think some of the material will be eventually available?

"Cell-estial bloom" Image from Özge Özgüç: A ‘Cell-estial bloom’ of human induced pluripotent stem cells (hiPSCs) flourishes on a micropatterned island. This image presents a colony of live hiPSCs, with fluorescently labelled Lamin B delineating the nuclear lamina within each cell. Acquired with a Zeiss LSM 880 Airyscan microscope, this maximum intensity projection is enhanced with depth-coded coloring to reveal the captivating three-dimensional landscape.

"Dancing actinotroch" by Allan Carrillo-Baltodano: Actinotroch larva of a phoronid worm with phalloidin shown in yellow and acetylated tubulin in magenta. Imaged with a Zeiss LSM 800 at 10 x magnification.

"Who’s active?" by Julia Peloggia de Castro: The image depicts a zebrafish embryo at 9 hours post-fertilisation on a lateral view. Cells are stained with MitoTracker, which labels active mitochondria, and cell membranes are labelled in cyan with a EGFP transgenic membrane tag. Image was taken using a 20x objective on a spinning disk confocal microscope.

🎉Congratulations to the Top 3 images from the Node–FocalPlane image competition!

1️⃣"Cell-estial bloom" by @oozguc.bsky.social
2️⃣"Dancing actinotroch" by @allancarbal.bsky.social
3️⃣"Who’s active?" by @jupeloggia.bsky.social

thenode.biologists.com/results-from...

@focalplane.bsky.social #biologists100

Overlay of good FF image with homogeneity and centrality scores

Overlay of a wrong cat picture instead of an FF image

As part of our regular health check of our systems at @istaustria-iof.bsky.social, we acquire and analyze flat-field images automatically through our internal database.

Today I noticed a particularly strange FF image my script analyzed, but of course I am going to leave it there! 😂

color-coded z projection of a weevil head acquired at Zeiss light-sheet 7 microscope

Let's give it a go to my first #FluorescenceFriday
Here's a color-coded Z-projection of a weevil head imaged on our Zeiss light-sheet 7 with pure green autofluorescence.

Looking very cool, but also ominous!

@istaustria-iof.bsky.social

Fiji 2024 Year in Review: Milestones and Roadmap Introduction The Fiji team at LOCI is pleased to share significant progress on several major initiatives as we work towards raising the technological standards of Fiji. These include Fiji 2.16.0, feat...

Wow, this is big: "Fiji can now be launched in a Python-first mode, where first Python is started, then Fiji is started via the PyImageJ library. In this mode, Fiji is fully integrated with the active Python environment"
forum.image.sc/t/fiji-2024-...

Update the Data Carpentries Bioimage Analysis with Python Curriculum Data Carpentries BioImage Analysis - update with a Python Curriculum Join us to update the Data Carpentries Bioimage Analysis Curriculum with a Python Curriculum! We’re inviting bioimage analysis prof...

Bioimage analysis professionals: join us in-person for a workshop at ISTA in Klosterneuburg, Austria, April 7–8, 2025. A workshop to adapt and expand the current Data Carpentries image processing curriculum. Information & registration: tinyurl.com/3twkax2k

Defense Against Dishonest Charts This is a guide to protect ourselves and to preserve what is good about turning data into visual things.

Dishonest charts are coming from all directions, and they're only going to hit harder. Unless we push back. So, an interactive guide: Defense Against Dishonest Charts flowingdata.com/projects/dis...

Is the first seminar on 13th February or March? I see contradicting info on the website ai4life.eurobioimaging.eu/events/

If you want to check out a plotting comparison I wrote some time ago with sample code :) mvgroup.gitlab.io/mvlearn/cont...

Join us in person for shaping the future of this already great curriculum! #globias #image-analysis #microscopy