Nellie: Automated organelle segmentation, tracking, and hierarchical feature extraction in 2D/3D live-cell microscopy
☆96May 15, 2026Updated 3 weeks 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 3 months ago
- Guides and code for 3D nuclear instance segmentation☆23Dec 2, 2025Updated 6 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 6 months 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 8 months ago
- The computational platform u-signal3D defines a shape-invariant representation of the spatial scales of molecular organization at the cel…☆11May 29, 2026Updated 2 weeks ago
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- 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☆31May 28, 2026Updated 2 weeks ago
- MultiModal Big Image Data Sharing and Exploration☆20Jan 13, 2023Updated 3 years ago
- Transformer-based cell tracking for live-cell microscopy☆130Mar 31, 2026Updated 2 months ago
- Software for Quantifying Mitochondrial Content in Live Cells☆31May 28, 2026Updated 2 weeks ago
- Denoising via adaptive binning.☆14Jan 6, 2026Updated 5 months ago
- Interprocess environment manager 🧊☆13May 11, 2026Updated last month
- Nanoscopy library for Python (NanoPyx, the successor to NanoJ) - focused on light microscopy and super-resolution imaging☆90Updated this week
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- A platform for compiling, analyzing, and exploring tracking data☆50Feb 2, 2026Updated 4 months ago
- Loading and handling microscopy data in blender☆154Updated this week
- Accurate and efficient spot detection for microscopy data☆130Feb 5, 2026Updated 4 months ago
- A napari plugin for clustering objects according to their properties.☆90Jun 1, 2026Updated last week
- A first intoduction to scripting in Fiji using the ImageJ Macro language.☆27Sep 26, 2024Updated last year
- A Python toolbox for registering / fusing / stitching large multi-view / multi-positioning image datasets in 2-3D.☆118Jun 2, 2026Updated last week
- A Python GUI-based framework for segmentation, tracking and cell cycle annotations of microscopy data☆197Updated this week
- Archives. Future development continues at SR-Wiki/SN2N.☆58Jan 15, 2026Updated 4 months ago
- Archived: control, reconstruction, and analysis code for oblique plane microscopy.☆23Apr 1, 2025Updated last year
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- MSSR Plugin☆14Oct 30, 2024Updated last year
- 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 4 years ago
- ☆14Jan 25, 2024Updated 2 years ago
- Handmade ImageJ / Fiji LUTs for microscopy, scientific good visualization and art.☆14Jan 9, 2025Updated last year
- The known BioVoxxel Toolbox functions now improved for 2D and 3D images☆20Feb 10, 2026Updated 4 months 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/…☆41Jun 4, 2026Updated last week
- napari plugin for trackastra☆18Updated this week
- ☆225Feb 4, 2026Updated 4 months ago
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- Multiple particle tracking in dense 3D particle fields complemented with dynamic regions of interest and trackability inferences for the …☆30May 29, 2026Updated 2 weeks ago
- ☆15Updated this week
- Icons describing multiple microscopy techniques, as used by https://www.epfl.ch/research/facilities/ptbiop/equipment/☆11Mar 13, 2023Updated 3 years ago
- ngio is a Python library to streamline OME-Zarr image analysis workflows.☆49Updated this week
- ☆22Updated this week
- A curated list of awesome Janelia software☆17Feb 26, 2025Updated last year
- ASHLAR: Alignment by Simultaneous Harmonization of Layer/Adjacency Registration☆175May 14, 2026Updated 3 weeks ago