I was searching for a Python utility for Fourier Ring/Shell Correlation. All I got in a blue sky search were 4 small posts from @christletx.bsky.social ... all I got from chatgpt was installation instructions for non-existent libraries and github repos... anyone know a good tool for this?

📢 After #CBIAS2025, join our hands-on 2-day napari training by @crick.ac.uk @ucl.ac.uk @liverpooluni.bsky.social From conda to plugins to Jupyter, practicals on real data with expert guidance. For Python/ImageJ coders. Apply by 1 Sept – limited to 30! crick.ac.uk/whats-on/cbias-napari-workshop-2025

Episode 11 - In which @erinweisbart.bsky.social and I talk about just how much we love ilastik (@ilastik-team.bsky.social) and how it's great for so many problems! Also, that you should use a small brush.

The 1st working version of my little @napari.org plugin (napari-czitools) is almost ready. It contains sample data, allows to read CZI metadata and can read CZI images (or parts of it) by using the sliders to crop what should be read. Still quite some things to improve ...

Cell tracking is never perfect, and it's important to understand the types of errors your solution contains. Here is my stab at this: Divisualisations in @napari.org. github.com/bentaculum/d... You spin tracks out upwards from the playing video. Green edges are correct, FP in magenta, FN in cyan.

I just published a new video demonstrating how to use Pixi and Napari-Easy-Augment-Batch-DL for repeatable and reproducible deep learning segmentation. In this example, I use Pixi to set up a Python environment then launch Napari to explore and compare Cellpose3 and Micro-SAM. youtu.be/3ObAnSTBri8

Great to see @alexhego.bsky.social share instructions on a DL pixel‑classification problem we worked on at image.sc. If you’re working on a challenging 3D DL semantic‑segmentation problem and need more options than most tools provide, check out this repository. github.com/AlexHego/DL-...

Btw, and in the spirit of #OpenScience, all my #Napari #bioimage analysis #tutorials are freely available — from basics to #segmentation, #tracking, and #clustering. Feel free to explore and share ✌️ 🌍 www.fabriziomusacchio.com/teaching/tea...

🚀 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

We released version 1.6 of micro_sam: - Improvements for automatic tracking. - A new experimental mode for object classification. - **New versions of the LM and EM models** The models fix artifacts in automatic segmentation, see old vs. new prediction and better 3D segmentation results due to it.

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

Need help with bioimage analysis? Contact the UK Euro-BioImaging Node to see how we can help! www.eurobioimaging-access.eu/nodes/uk-node

Want to host your own AI models without relying on external infrastructure? Enter BioEngine ai4life.eurobioimaging.eu/announcing-b... Your go-to for flexible, self-hosted bioimage analysis. Open source, scalable, and built for you!

I've started a thread on the imagesc forum about how ambiguous labels might affect deep learning models. If you've encountered mislabeled data, strange training artifacts, or examples where the former caused the latter — I'd love to hear your insights. forum.image.sc/t/are-we-see...

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!

Reminder: if you go to the GloBIAS conference we can help you contribute to napari at the hackathon! A bunch of the team will be there! (Great thanks to the GloBIAS team for accommodating us!!!) More details on the conference website.

Episode 5 - sure, most cells have one nucleus, but what happens when they DON'T? @erinweisbart.bsky.social and I try to get to the bottom of what on earth you can do when your cells and nuclei just don't match up on the latest episode of "Ask Erin/Dear Beth"

This is a nice overview of normalization techniques which are very important for deep learning training. It is pretty common that differences in the training and testing image intensity ranges lead to unpredictable errors so learning to troubleshoot normalization issues is very useful.

Just uploaded a simple script to run cellpose for cell segmentation on two-photon calcium imaging data and extract ΔF/F traces. It runs slower without a GPU, but still works well. Check it out and give it a try! github.com/dav1dcg/neur...

We are proudly hosting 𝐃𝐫. 𝐓𝐚𝐥𝐥𝐞𝐲 𝐋𝐚𝐦𝐛𝐞𝐫𝐭 @talley.codes (CITE, Harvard Medical School): 𝐒𝐢𝐦𝐮𝐥𝐚𝐭𝐢𝐧𝐠 𝐫𝐞𝐚𝐥𝐢𝐬𝐭𝐢𝐜 𝐥𝐢𝐠𝐡𝐭 𝐦𝐢𝐜𝐫𝐨𝐬𝐜𝐨𝐩𝐲 𝐢𝐦𝐚𝐠𝐞𝐬 𝐮𝐬𝐢𝐧𝐠 𝐦𝐢𝐜𝐫𝐨𝐬𝐢𝐦 When: 𝐌𝐚𝐲 𝟐𝟗𝐭𝐡 @ 𝟏𝟏 𝐚𝐦 𝐄𝐃𝐓 (Boston time) Join us on Zoom! harvard.zoom.us/j/9762343464...

💻 Apply to our beginner-friendly Boston Bioimage Analysis Course! Get started with Python and learn to analyze fluorescence microscopy images — no coding experience required! Fee waivers available thanks to funding from @bioimagingna.bsky.social! 🗓️ Apply June 1st! iac.hms.harvard.edu/bobiac/2025/

Wow, just implemented the new Cellpose-SAM from @computingnature.bsky.social in NimbusImage and it's *awesome*! Give it a try! nimbusimage.com

Want to learn more about bioimage analysis and how to think like a bioimage analyst? Check out our bootcamp- applications close next week!

So excited and proud of everyone! 🎉 With this release I worked very hard to contribute to napari and learned so much along the way. I guess they want to keep me around, as I'm a core dev now! 🥳 Grateful for the entire image analysis community. 🥰

In case you were wondering where the "Tools" menu is gone in @napari.org 0.6.0, please update your environment using "pip install napari-assistant==0.6.0". Then just start "naparia" instead of "napari" from the terminal, while we are working on a better solution. github.com/haesleinhuep...

Still plenty of time before first pitch to check out today’s new episode of Deep Left Field! Tremendous conversations with #Bluejays Anthony Santander and Brendon Little plus coach Mark Budzinski! Also, a look back at a week that was that started and ended awfully well, but in the middle - yuck.

Finally BiaPy is out in Nature Methods! 🥳🥳🥳 A major milestone in my research! I'm incredibly proud of the progress made. Huge thanks to my PhD supervisors, @iarganda.bsky.social and @arratemunoz.bsky.social , for their invaluable guidance and support throughout this journey. Check out the thread🧵👇

During the workshop earlier this week we discussed how important it is to inspect histograms of image regions in some projects. Thus, here comes stackview.histogram() - new in stackview 0.15.0 🥳 github.com/haesleinhuep...

If you are looking to do GPU deconvolution in Fiji checkout the new updates to CLIJ (OpenCL for ImageJ) deconvolution. @nkiaru.bsky.social has done updates to the tiled deconvolution and integrated with BigDataViewer, and I've added a new script for batch processing. forum.image.sc/t/clij-openc...

For the last couple of years I've been developing DL segmentation utilities, workflows and notebooks with the goal of making it easier to reproduce deep learning results. This new video shows how to run augmentation, training and prediction all inside Napari www.youtube.com/watch?v=ngps...

The OME Community Meeting, which has always be in Europe, will be at MBL this year! It's a unique opportunity for people this side of the pond who are working with open-source microscopy data. Travel grants available for NA-based folks until Feb 12th! www.bioimagingnorthamerica.org/events/ome-2...

There's a new wave of discussion to improve the clarity of Fiji's original menus and plugins. If you have opinions or suggestions to make, don't hesitate to participate on the forum! forum.image.sc/t/houseclean... #microscopy #imagej #fiji

If anyone is interested in obtuse observations about 3D SIM reconstruction I've added some more figures to my thread on 3D SIM see here forum.image.sc/t/3d-sim-rec.... In particular I took a look at results from different stages of Open3DSIM github.com/Cao-ruijie/O...

A very nice #MachineLearning example from Fiji Weka Segmentation. Was just playing with this plugin today on another problem and it works great.

Today I would like to highlight one of our favorite DL-segmentation network: StarDist by @maweigert.bsky.social and colleagues. In my lab we love and use StarDist all the time github.com/stardist/sta... link.springer.com/chapter/10.1... #BioimageTooloftheDay

Contributing to this project has been very cool! Quick tip for anyone interested in cell segmentation: I started with StarDist but it failed to detect nuclei in samples with regions of very different cell density. Switched to DeepCell Mesmer and it worked like a charm!

For people interested with a PyImageJ install also containing cellpose in the same environment, a singularity container (the file to build it) bound to 'da_tracker' is available on github now. A link to download the built container can be found as well on the main page. github.com/jaugenst/da_... 👇

This week I tested pixel based machine learning using a Napari plugin written by @kephale.bsky.social , and posted a video of my experiments (interestingly Herbie G. may have beat both DL and ML with an ImageJ Macro on one of the test images) youtu.be/9rnNDkvVUyY

Tomorrow morning I will give a webinar talk + Q&A for the Microscopy Society of America. Tuesday 17 Dec at 8 am PT / 11 am ET. Registration free: microscopy.org/Events/detai...

I just made a long overdue update to microfilm guiwitz.github.io/microfilm now 0.3.0! Beyond adaptations to recent Python and Matplotlib, I added support for the great cmap library cmap-docs.readthedocs.io by @talleylambert.bsky.social for easy access to the best (and most psychedelic) colormaps!1/2

I finally got around to making a video about my utilities to render 3D projections in Jupyter notebooks. The code is useful but a bit rough so I also suggest taking a look at @guiwitz.bsky.social microfilm and @haesleinhuepf.bsky.social stackview as more polished options. youtu.be/9yOA8R03trE

1) I was looking for a basic Machine Learning pixel classification example the other day, and example '02' in this @haesleinhuepf.bsky.social repo is a nice starting point, simple, can get it running in few minutes, and great to start learning about the subject. github.com/BiAPoL/on_th...

Update. It looks like upgrading to Cellpose 3.1.0 solves some of the issues. 3.1.0 has new options for smoothing masks and the 3D mask generation is much faster. See this post forum.image.sc/t/cellpose-3.... Thanks @computingnature.neuromatch.social.ap.brid.gy and others for the new release.

#MicroscopeMonday by Raphael for our first post on bluesky here's our new image processing available on our OpenCID database: you can now directly run #denoise #deblur #upsample with the new version of cellpose on all your images thanks to the #cellpose team for their always top-notch dev

forum.image.sc/t/cellpose-3... Interesting forum question on 3D Cellpose that isn't answered yet. I played around a bit this morning but couldn't quite figure it out. Love to hear from others who work with 3D Cellpose (or other 3D segmentation methods)

There's just over a month left to apply for our upcoming @royalmicrosoc.bsky.social Introduction to Image Analysis workshop with @martinjones.bsky.social and @lankylaste.bsky.social hosted by @kerrythompson8.bsky.social at @uniofgalway.bsky.social www.rms.org.uk/rms-event-ca...

There are also different implementations of the Tubeness Filter. One is already in ImageJ available ( Plugins › Analyze › Tubeness). The other in the amazing CLIJ2 library from @haesleinhuepf.bsky.social which I will surely feature various times again in the future.

#BIAToolTip No.13 A Must-Know: the amazing CLIJ2 library from @haesleinhuepf.bsky.social and its IJ macro extensions make image processing and analyses of 2D/3D images on the GPU a breeze and super flexible. Huge function repository, a very neat clij2 assistant and super easy to macro record.

Are you interested in doing 3D microscopy? I will be showing on Dec 10 how I use high-resolution microscopy combined with 3D reconstruction to investigate neurodegeneration and neuroinflammation in the brain, especially with viral infections! Register here: register.gotowebinar.com/register/636...

My #BioimageTooloftheDay is an easy one: Cellpose by @computingnature.neuromatch.social.ap.brid.gy and colleagues An awesome DL-segmentation network to segment cells from microscopy images www.nature.com/articles/s41... When we do not use StarDist, we use Cellpose 😀