Basic example of using OME-Zarr in a Nextflow pipeline
☆20Jul 15, 2025Updated 7 months ago
Alternatives and similar repositories for ome-zarr-image-analysis-nextflow
Users that are interested in ome-zarr-image-analysis-nextflow are comparing it to the libraries listed below
Sorting:
- A collection of Image Processing and Analysis (IPA) functions used at the Facility for Advanced Imaging and Microscopy (FAIM)☆18Feb 23, 2026Updated last week
- Paint segmentations directly to on-disk/remote zarr arrays☆15Jun 26, 2024Updated last year
- Pydantic models for OME-NGFF☆24Sep 14, 2025Updated 5 months ago
- Create web-based OME-Zarr galleries☆22Nov 6, 2025Updated 3 months ago
- Robust and unbiased estimation of the background distribution for fluorescence microscopy.☆13Oct 13, 2025Updated 4 months ago
- ☆23Mar 26, 2021Updated 4 years ago
- Efficient graph data structures and algorithms for fast slicing, visualization, and editing☆13Dec 1, 2025Updated 3 months ago
- Raw format to OME-TIFF converter☆56Feb 18, 2026Updated 2 weeks ago
- Block-wise operations for large nD volumes☆45Feb 25, 2026Updated last week
- A data pipeline built in Nextflow to process spatial and single-cell experiment data for visualisation in WebAtlas☆67Jul 2, 2025Updated 8 months ago
- An application to display spatial and single-cell experiment data. Built in React, on the Vitessce framework.☆14Nov 3, 2025Updated 4 months ago
- ☆41Feb 13, 2026Updated 2 weeks ago
- Ngio is a Python library to streamline OME-Zarr image analysis workflows.☆42Feb 23, 2026Updated last week
- A napari plugin to load & deskew folders of lattice light sheet TIFFs☆13Jan 5, 2026Updated last month
- A 3D interactivity toolbox for napari☆37Jul 8, 2025Updated 7 months ago
- Gamified image segmentation quality estimation☆19May 1, 2025Updated 10 months ago
- A napari plugin for zarr backed OME-NGFF images☆44Feb 23, 2026Updated last week
- A dataset for loading zarr files to be used in machine learning training pipelines☆35Jan 5, 2026Updated last month
- GIve easy, high-level access to ome-zarr fileset☆22Sep 22, 2025Updated 5 months ago
- Project planning and material repository for the 2024 challenge to generate 1 PB of OME-Zarr data☆21Jan 9, 2026Updated last month
- Implementation of next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.☆225Feb 23, 2026Updated last week
- 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
- ☆18Feb 24, 2026Updated last week
- ☆20Updated this week
- Get Your Brain Together Neuroimage Registration Workshops and Hackathons☆21Nov 14, 2024Updated last year
- Accelerated Pixel and Object Classifiers (APOC)☆60Jul 18, 2025Updated 7 months ago
- Graph-based framework to manipulate and analyze cell lineages from cell tracking data☆24Feb 20, 2026Updated last week
- Generate multifunctional and macro recordable GUIs from Python classes☆45Nov 16, 2025Updated 3 months ago
- native Python dataclasses for the OME data model☆65Feb 12, 2026Updated 2 weeks ago
- Guides and code for 3D nuclear instance segmentation☆23Dec 2, 2025Updated 3 months ago
- A JupyterBook site for napari workshop materials☆10Jul 11, 2022Updated 3 years ago
- A stable diffusion demo for napari☆11Dec 15, 2023Updated 2 years ago
- ITK IO for images stored in OME-Zarr format.☆11Sep 4, 2025Updated 6 months ago
- Running ImJoy plugins in Jupyter notebooks☆11Jan 10, 2023Updated 3 years ago
- A napari Plugin for visualisaton of pixel values over time (t+ nD) as graphs.☆12Apr 24, 2024Updated last year
- An automated point-set based registration algorithm for correlative light and electron microscopy (CLEM)☆21Oct 22, 2025Updated 4 months ago
- Cookiecutter for napari plugins☆71Nov 6, 2024Updated last year
- Image reading, metadata management, and image writing for Microscopy images in Python☆114Dec 22, 2025Updated 2 months ago
- dask empowered fast4dreg☆15Feb 20, 2026Updated last week