#cellpose Suchergebnisse

4/14🔬 We captured 16-to 22-hour 3D movies of this process. However, segmenting and tracking individual cells in a dense 3D tissue is a challenging task. We built a deep learning pipeline that combines the forces of #StarDist, #UNET, #Cellpose, and #TrackMate. 💪#ImageAnalysis

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/ann… #bioimageanalysis #cellpose #imaging #HowTo

🖥️ A new version of #Cellpose – the popular tool developed by @computingnature & @marius10p that maps the boundaries of diverse cells in microscopy images – now works on less-than-perfect pictures that are noisy, blurry, or undersampled. 🔗janelia.org/news/newest-ve…

We took a “no cell shall be left behind” approach which wouldn’t be possible without #Cellpose, #TrackMate, #Fiji and advanced #rstats analysis and visualization with #GlmmTMB, #emmeans and #SuperPlots

When you're training #cellpose models by day and #microsam models by night tenor.com/bmRuU.gif

Read about our experience and that of others in building software for biology. #kilosort #suite2p #cellpose #facemap #rastermap

GLOMTAGE!!! Glomeruli > From scratch #cellpose Tissue type > @ilastik_team Nuceli > #stardist Automation > @FijiSc And now the decicion on how many parameters to log out, @MilesDeBlasio that one is up to you. (Ok, I'll see myself out over the glomtage name) :)

Thank you @NerdyCammy your @FijiSc and Friends ML book has opened the door to making #CellPose models - a gentle guide through setting up Anaconda, Powershell etc. can’t wait to get started on my data!

#FluorescenceFriday by Martin R @OpenCID expands its integrated processing and analysis offering. You can now launch @QuPath with #Cellpose or #Stardist for #deeplearning #segmentation of all your pyramid images from all your microscopes or scanners, fluo or BF #HistoCytometry

One of the most popular talks at the Boston #NextflowSummit comes to blog format! Check out how to use the @nf_core #molkart pipeline with #Cellpose on @SeqeraLabs Data Studios - it's pretty slick!

The analysis pipeline (@nf_core #molkart) and the interactive software (#Cellpose) are both open source, see links in the article. The Data Studios feature that it's running within is part of @SeqeraLabs Platform. That's not OSS, but it is free (incl. free pro plan for academics)

3/ 🔬 #Ultrack can use input segmentations produced by any segmentation algorithm, such as #Cellpose, #Stardist, ... and can even combine their results to maximize tracking accuracy. It can also work directly on images in which the boundaries of cells are labeled (e.g.,…

The PowerPoint slides (in English, CC-BY licensed) from my talk on open-source AI tools for bioimage analysis are now available on Zenodo. This is Part III, continuing from previous works. Feel free share! doi.org/10.5281/zenodo… #ilastik #StarDist #Cellpose #SAMJ

This is a fantastic introductory post for anyone interested in using #cellpose or #StarDist within #Cellprofiler! ⤵️

Do you use CellProfiler to analyse your images and have been curious to experiment with deep-learning-based segmentation algorithms (#Cellpose and #StarDist)? I wrote a blogpost carpenter-singh-lab.broadinstitute.org/blog/leveragin… to help complete beginners use these plugins in #cellprofiler! #imageanalysis

4/ Imagine asking #Omega to "segment cell nuclei in the selected image" and following up with post-analysis that would have otherwise required code! It can handle both 2D and 3D images with ease leveraging popular packages such as #StarDist or #CellPose. Here’s an example in 2D:…

It's good to have friends. A new training manual and resources have joined the collection. Hooking @Fiji in with AI/ML tools like #N2V, #cellpose, #stardist and @ilastik_team Includes notes on instalation, setup, use and training models. Links to everything in the comments.

Using grey value changes as a proxy for curvature to infer 3D information from a 2D image. Using @napari_imaging and #CellPose (@computingnature) #elmi2024

Phwoar #cellpose basic install guide would be magic. I feel like as a biologist it's beyond my ability to install/use.

Thanks :) Stay tuned for the upcoming @FijiSc and Friends edition with notes on using #startdist, #cellpose and @ilastik_team

Releasing Cellpose 2.0 today! You can now train your own state-of-the-art models in <1h, all from the GUI. Massive improvements for some images! paper: biorxiv.org/content/10.110… code: github.com/MouseLand/cell… Full story below 👇. #cellpose with @computingnature

Positions for remote work available to help us with #suite2p, #kilosort2 or #cellpose. Start date flexible.

Thanks to #Cellpose you can also segment stem cells

Cellpose 2.0: how to train your own model "State-of-the-art cellular segmentation does not require big data"😎 "Human-in-the-loop" protocol #Cellpose Dr. Marius Pachitariu & Carsen Stringer @naturemethods 2022 @marius10p @computingnature nature.com/articles/s4159…

Made a little pipeline using #Cellpose and a @FijiSc batch-analysis macro to automate evaluation of single-cell YAP nucleus/cytosol mean intensity ratios in 2D images. #Cellpose is AMAZING! Nuclei labels originally obtained with #Stardist, but Cellpose also does a great job.

#cellpose

It's amazing how accurately #CellPose is segmenting my cells! @marius10p

#FluorescenceFriday by Gabriel 40000 nucleus segmented automatically thanks #CellPose !!! @InstitutCochin

with a beautiful segmentation with #Cellpose

Having a blast with #omnipose #cellpose @KevinJohnCutler @computingnature 🤓😍

We've added 3D segmentation to #cellpose. No 3D training data needed! Updated preprint: biorxiv.org/content/10.110… Code: github.com/MouseLand/cell…

#EMBOBioimage @napari_imaging #cellpose Who said cell segmentation was difficult? 🤩 Napari+cellpose

#FluorescenceFriday by Raphael @Fr_BioImaging @imag_ic @IJMonod after the integration of @svi_huygens and @BioimageIT you can now use #Cellpose to segment all your images stored in #CochinImageDatabase in just 2 clicks @InstitutCochin @CNRS @EuroBioImaging @univ_paris_cite

#Cellpose segmenting cell monolayer imaged in phase contrast at 10X magnification, not bad...

Version (0.7.0) of the wrappers for Fiji including #cellpose #stardist 3D (and 2D) works on MacOS 🤞(at least in CPU mode 😅) #bioimageanalysis #Fiji github.com/BIOP/ijl-utili…

You try #cellpose yet?

ANNNND fed the max projection into #Cellpose & masking worked like a charm. So thrilled 🤩.

Taking the RER after a day working with #cellpose 2.0

*Cellpose: a generalist algorithm for cellular segmentation*, now out in @naturemethods with new analyses! Looking forward to seeing what y’all do with it. With @marius10p, #NotTheCover #cellpose nature.com/articles/s4159…

C'est partie pour toute l'équipe @imag_ic direction #MiFoBio2023 ! On se retrouve toute la semaine : A78 #STEDFLIM A40 #CellPose TR178 #Qualité #Bar_à_Image #OpticLab Et devant tous nos Posters À très vite !!