Nellie: Automated organelle segmentation, tracking, and hierarchical feature extraction in 2D/3D live-cell microscopy
☆98May 15, 2026Updated 4 months ago
Alternatives and similar repositories for nellie
Users that are interested in nellie are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- ☆12Feb 23, 2026Updated 6 months ago
- Guides and code for 3D nuclear instance segmentation☆23Dec 2, 2025Updated 9 months ago
- A short course exploring several fun and useful notebooks and Napari widgets for deep learning with SAM, Cellpose, Stardist and friends.☆19Dec 9, 2025Updated 9 months ago
- MultiModal Big Image Data Sharing and Exploration☆20Jan 13, 2023Updated 3 years ago
- Segmentation method able to detect membrane/nuclei-labelled cells with low signal-to-noise ratio and dense packing in 2D and 3D. Availabl…☆34Oct 8, 2025Updated 11 months ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- Interactive visualization and sharing of cell tracking data in the browser☆48Aug 24, 2026Updated 3 weeks ago
- The computational platform u-signal3D defines a shape-invariant representation of the spatial scales of molecular organization at the cel…☆11May 29, 2026Updated 3 months ago
- Deep Learning segmentation suite designed for 2D microscopy image segmentation☆10Dec 17, 2021Updated 4 years ago
- Microsnoop: A generalist tool for microscopy image representation☆13Feb 27, 2025Updated last year
- FIJI plugin for tracing of curvilinear structures in volumetric microscopy datasets☆31Sep 7, 2026Updated 2 weeks ago
- Denoising via adaptive binning.☆14Aug 28, 2026Updated 3 weeks ago
- Nanoscopy library for Python (NanoPyx, the successor to NanoJ) - focused on light microscopy and super-resolution imaging☆93Aug 24, 2026Updated 3 weeks ago
- A platform for compiling, analyzing, and exploring tracking data☆50Feb 2, 2026Updated 7 months ago
- Loading and handling microscopy data in blender☆161Aug 24, 2026Updated 3 weeks ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- Software for Quantifying Mitochondrial Content in Live Cells☆32May 28, 2026Updated 3 months ago
- Block-wise operations for large nD volumes☆45Updated this week
- Archived: control, reconstruction, and analysis code for oblique plane microscopy.☆23Apr 1, 2025Updated last year
- A Python toolbox for aligning / fusing / stitching large multi-view / multi-positioning image datasets in 2-3D.☆134Sep 6, 2026Updated 2 weeks ago
- ☆243Jul 30, 2026Updated last month
- A first intoduction to scripting in Fiji using the ImageJ Macro language.☆27Sep 26, 2024Updated last year
- A napari plugin for clustering objects according to their properties.☆90Sep 14, 2026Updated last week
- Accurate and efficient spot detection for microscopy data☆143Jun 8, 2026Updated 3 months ago
- A Python GUI-based framework for segmentation, tracking and cell cycle annotations of microscopy data☆202Updated this week
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- computer vision models for single-cell phenotyping☆104Updated this week
- Cell tracking and segmentation software☆209Aug 13, 2026Updated last month
- MSSR Plugin☆14Oct 30, 2024Updated last year
- Archives. Future development continues at SR-Wiki/SN2N.☆62Jan 15, 2026Updated 8 months ago
- SciCount is tool focused on counting and classifying of objects in image-like data and scientific images, with training and example datas…☆11Oct 24, 2023Updated 2 years ago
- A Fiji/ImageJ plugin to generate ROIs from label images, allowing ROI erosion and quantification☆23Sep 11, 2021Updated 5 years ago
- ☆14Jan 25, 2024Updated 2 years ago
- Fast4DReg is a Fiji script for quick drift correction in time-lapse 3D-stacks. The script can be used to correct drift in all x-, y- and/…☆41Aug 7, 2026Updated last month
- The known BioVoxxel Toolbox functions now improved for 2D and 3D images☆21Feb 10, 2026Updated 7 months ago
- Open source password manager - Proton Pass • AdSecurely store, share, and autofill your credentials with Proton Pass, the end-to-end encrypted password manager trusted by millions.
- Handmade ImageJ / Fiji LUTs for microscopy, scientific good visualization and art.☆16Jan 9, 2025Updated last year
- Napari plugin for custom analysis and visualization of lattice lightsheet and Oblique Plane Microscopy data. The plugin is optimized for …☆19Sep 10, 2026Updated last week
- napari plugin for trackastra☆19Jul 16, 2026Updated 2 months ago
- Interprocess environment manager 🧊☆17May 11, 2026Updated 4 months ago
- ☆22Updated this week
- Multiple particle tracking in dense 3D particle fields complemented with dynamic regions of interest and trackability inferences for the …☆32May 29, 2026Updated 3 months ago
- Official implementation of MuViT (CVPR 2026), a ViT-based architecture for multi-scale modelling of gigapixel microscopy images.☆48Jun 7, 2026Updated 3 months ago