WEBKNOSSOS: Visualize, share and annotate your large 3D images online Visualize, share, and annotate your large 3D images online. Upload your data and share links with colleagues. Collaboratively create skeleton and volume annotations, all from your browser. Optimized f...

My #BioimageTooloftheDay is webKnossos weblium.webknossos.org
It's an awesome annotation tool to do manual segmentation of 3D FIB-SEM dataset. While we cannot quite afford the pro version, the free version will already take you far.

Introduction to Bioimage Analysis — Introduction to Bioimage Analysis

My #BioimageTooloftheDay
is the fantastic Introduction to Bioimage Analysis book by Pete Bankhead
bioimagebook.github.io/index.html
Because seriously, this is awesome
Also how can you get started without a good book

My #BioimageTooloftheDay is the fantastic AFT-Alignment tool
www.frontiersin.org/journals/com...

github.com/OakesLab/AFT...

We used the Python implementation to study actin stress fibers organisation in endothelial monolayers

GitHub - fiji/Kappa: A Fiji plugin for Curvature Analysis A Fiji plugin for Curvature Analysis. Contribute to fiji/Kappa development by creating an account on GitHub.

My #BioimageTooloftheDay is Kappa, a neat Fiji plugin we used to measure curvature
github.com/fiji/Kappa

GitHub - segment-anything-models-java/SAMJ-IJ: An ImageJ/Fiji plugin designed to effortlessly integrate Segment-Anything models (SAMs) without code. An ImageJ/Fiji plugin designed to effortlessly integrate Segment-Anything models (SAMs) without code. - segment-anything-models-java/SAMJ-IJ

My #BioimageTooloftheDay is SAMJ-IJ a wonderful image annotator for Fiji
github.com/segment-anyt...

GitHub - volume-em/empanada-napari: Panoptic segmentation algorithms for 2D and 3D electron microscopy in napari Panoptic segmentation algorithms for 2D and 3D electron microscopy in napari - volume-em/empanada-napari

My #BioimageTooloftheDay is empanada-napari
A very well-designed and useful Napari plugin to segment mitochondria from EM images
github.com/volume-em/em...

www.cell.com/cell-systems...

"NeuroCyto LUTs" update site Hi, as a LUTs afficionado I have collected and designed a lot of LUTs and found the built-in menu difficult to organize. So I’ve made a specific LUTs menu (using a folder in the “scripts” folder, fill...

My #BioimageTooloftheDay is the NeuroCyto Luts Fiji plugin by @christlet.bsky.social

A must have collection of very useful LUT to make beautiful merge images

forum.image.sc/t/neurocyto-...

As my first post, I am reposting from Twitter our Phindr3D (slightly rewritten).
#BioimageTooloftheDay. Phindr3D is a comprehensive #ShallowLearning framework for automated quantitative phenotyping of #3D #HighContentScreening images. Still valuable in the age of (un)explainable #deeplearning.😉

My #BioimageTooloftheDay is QuimP a software for tracking cellular shape changes and dynamic distributions of fluorescent reporters at the cell membrane.
Also makes beautiful cover images warwick.ac.uk/fac/sci/dcs/...

My #BioimageTooloftheDay is DRMIME
github.com/abnan/DRMIME
It is a very useful tool for aligning images.
I had a lot of fun using it to align zebrafish embryos.
Also available on #ZeroCostDL4Mic
github.com/HenriquesLab...

NanoJ: a high-performance open-source super-resolution microscopy toolbox Super-resolution microscopy (SRM) has become essential for the study of nanoscale biological processes. This type of imaging often requires the use of specialised image analysis tools to process a lar...

My #BioimageTooloftheDay is NANOJ by @henriqueslab.bsky.social lab. NanoJ is super useful for several application including image registration pmc.ncbi.nlm.nih.gov/articles/PMC...

NanoJ had a massive impact on our work and inspired for instance Fast4DReg

F1000Research Article: Bleach correction ImageJ plugin for compensating the photobleaching of time-lapse sequences. Read the latest article version by Kota Miura, at F1000Research.

My #BioimageTooloftheDay is the Bleach correction ImageJ plugin f1000research.com/articles/9-1...

Very useful yet rarely praised.

TrackMate TrackMate is your buddy for your everyday tracking.

My #BioimageTooloftheDay is TrackMate by @jytinevez.bsky.social and co
We use TrackMate in the lab all the time :)
I was also lucky enough to work with JY on one the iteration of this fantastic Fiji plugin
imagej.net/plugins/trac...

Fpbioimage The ImageJ wiki is a community-edited knowledge base on topics relating to ImageJ, a public domain program for processing and analyzing scientific images, and its ecosystem of derivatives and variants...

My #BioimageTooloftheDay is FPBioimage, a very useful tool for viewing volumetric data
It has a Fiji plugin that works well. The best feature is that you can easily tune rendering quality so you can view larger datasets even without GPU. imagej.net/plugins/fpbi...
fpb.ceb.cam.ac.uk

3Dscript: animating 3D/4D microscopy data using a natural-language-based syntax - Nature Methods Nature Methods - 3Dscript: animating 3D/4D microscopy data using a natural-language-based syntax

My #BioimageTooloftheDay is the awesome 3Dscript that I use to make video of 3D/4D microscopy data www.nature.com/articles/s41...

The best thing is that ChatGTP (probably other LLM) synergies beautifully with 3Dscript, making it ever easier to use. Voice to 3D video animation 😁

Cellpose 2.0: how to train your own model - Nature Methods Cellpose 2.0 improves cell segmentation by offering pretrained models that can be fine-tuned using a human-in-the-loop training pipeline and fewer than 1,000 user-annotated regions of interest.

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 😀

GitHub - stardist/stardist: StarDist - Object Detection with Star-convex Shapes StarDist - Object Detection with Star-convex Shapes - stardist/stardist

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

Labkit - Intuitive Pixel Classification in Fiji The ImageJ wiki is a community-edited knowledge base on topics relating to ImageJ, a public domain program for processing and analyzing scientific images, and its ecosystem of derivatives and variants...

Today I would like to highlight Labkit from @florianjug.bsky.social lab, one of my favorite pixel classifier. Fiji plugin, very easy to use, GPU accelerated, works on large datasets and has batch processing. imagej.net/plugins/labk...
www.frontiersin.org/journals/com...
#BioimageTooloftheDay

Distance Analysis The ImageJ wiki is a community-edited knowledge base on topics relating to ImageJ, a public domain program for processing and analyzing scientific images, and its ecosystem of derivatives and variants...

Today I want to highlight another very useful Fiji plugin Distance Analysis (DiAna).
We used it in a couple of papers already
imagej.net/plugins/dist...

www.sciencedirect.com/science/arti...

#BioimageTooloftheDay

GitHub - BIOP/ijp-LaRoMe: some useful function to get Label from ROIs and vice versa , and more! some useful function to get Label from ROIs and vice versa , and more! - BIOP/ijp-LaRoMe

I will try to take on the challenge to highlight some of the cool bioimage analysis tools we use all the time. #BioimageTooloftheDay

I will start with ijp-LaRoMe, a very nifty Fiji plugin that I use all the time to convert ROI to label images and vice versa
github.com/BIOP/ijp-LaR...