GitHub topics: napari
tlambert03/napari-omero
Browse your OMERO database from within napari.
Language: Python - Size: 9.67 MB - Last synced at: about 6 hours ago - Pushed at: about 7 hours ago - Stars: 37 - Forks: 14
napari/napari
napari: a fast, interactive, multi-dimensional image viewer for python
Language: Python - Size: 78.3 MB - Last synced at: about 15 hours ago - Pushed at: about 19 hours ago - Stars: 2,355 - Forks: 439
computational-cell-analytics/micro-sam
Segment Anything for Microscopy
Language: Jupyter Notebook - Size: 55 MB - Last synced at: about 11 hours ago - Pushed at: about 11 hours ago - Stars: 541 - Forks: 67
baltuni/Calcium-Correlation-Tool Fork of Angsas/Calcium-Correlation-Tool
Cell segmentation and tracking pipeline for time-lapse microscopy data using Cellpose. Includes segmentation, tracking, and correlation analysis of cell properties over time.
Language: Jupyter Notebook - Size: 3.9 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 3 - Forks: 0
Kapoorlabs-CAPED/NapaTrackMater
Napari Visualization tool for Trackmate > 6.0 XML files for 2/3D + time tracks. Available via pip package napatrackmater.
Language: Python - Size: 60.9 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 16 - Forks: 4
matplotlib/napari-matplotlib
Linking napari layers with Matplotlib plots
Language: Python - Size: 9.1 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 40 - Forks: 22
pymmcore-plus/napari-micromanager
GUI interface between napari and micromanager powered by pymmcore-plus and pymmcore-widgets
Language: Python - Size: 2.53 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 67 - Forks: 21
scverse/napari-spatialdata
Interactive visualization of spatial omics data
Language: Python - Size: 45.4 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 55 - Forks: 18
4DNucleome/PartSeg
Tool for segmentation in bioimaging
Language: Python - Size: 32.7 MB - Last synced at: 6 days ago - Pushed at: 7 days ago - Stars: 31 - Forks: 11
clEsperanto/napari_pyclesperanto_assistant
GPU-accelerated general purpose image processing and image analysis in napari
Language: Python - Size: 116 MB - Last synced at: 6 days ago - Pushed at: 11 days ago - Stars: 35 - Forks: 9
haesleinhuepf/napari-skimage-regionprops
Feature extraction for labeled objects in images using regionprops from scikit-image
Language: Python - Size: 38.3 MB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 50 - Forks: 13
brainglobe/brainglobe-segmentation
Segmentation of anatomical structures in a common coordinate space
Language: Python - Size: 11.1 MB - Last synced at: 11 days ago - Pushed at: 12 days ago - Stars: 31 - Forks: 11
napari/napari-plugin-manager
napari plugin manager to provide a graphical user interface for installing napari plugins.
Language: Python - Size: 1.95 MB - Last synced at: 13 days ago - Pushed at: 13 days ago - Stars: 8 - Forks: 8
BioimageAnalysisCoreWEHI/napari_lattice
Napari plugin for custom analysis and visualization of lattice lightsheet and Oblique Plane Microscopy data. The plugin is optimized for data from the Zeiss lattice lightsheet microscope.
Language: Jupyter Notebook - Size: 181 MB - Last synced at: 15 days ago - Pushed at: 15 days ago - Stars: 13 - Forks: 4
sebi06/python_envs
This repository contains a collection of YML and/or requirments file and tricks to create Python Environments
Size: 80.1 KB - Last synced at: 18 days ago - Pushed at: 18 days ago - Stars: 0 - Forks: 1
brisvag/blik
Python tool for visualising and interacting with cryo-ET and subtomogram averaging data.
Language: Python - Size: 2.46 MB - Last synced at: 4 days ago - Pushed at: 5 months ago - Stars: 25 - Forks: 8
pkosurilab/BellaVista
Python package for interactive visualization of imaging-based spatial transcriptomics
Language: Python - Size: 96.5 MB - Last synced at: 19 days ago - Pushed at: 5 months ago - Stars: 4 - Forks: 0
psobolewskiPhD/napari_scripts
Collection of useful (to me) python scripts for interacting with napari
Language: Python - Size: 47.9 KB - Last synced at: 28 days ago - Pushed at: over 2 years ago - Stars: 8 - Forks: 3
brainglobe/brainreg-napari 📦
Automated 3D brain registration in napari with support for multiple species and atlases.
Language: Python - Size: 116 KB - Last synced at: 6 days ago - Pushed at: over 1 year ago - Stars: 16 - Forks: 6
imagej/napari-imagej
Use ImageJ functionality from napari
Language: Python - Size: 3.94 MB - Last synced at: 28 days ago - Pushed at: about 1 month ago - Stars: 29 - Forks: 5
napari/napari.github.io
website for the napari image viewer
Size: 11.6 GB - Last synced at: about 17 hours ago - Pushed at: about 18 hours ago - Stars: 44 - Forks: 44
deep-finder/napari-deepfinder
A napari plugin for the DeepFinder library which includes display, annotation, target generation, segmentation and clustering functionalities. An orthoslice view has been added for an easier visualisation and annotation process.
Language: Python - Size: 5.5 MB - Last synced at: 8 days ago - Pushed at: about 1 month ago - Stars: 3 - Forks: 1
junlabucsd/napari-mm3
Mother machine image analysis through napari
Language: Jupyter Notebook - Size: 20.1 MB - Last synced at: 6 days ago - Pushed at: 3 months ago - Stars: 10 - Forks: 4
hanjinliu/impy
Speed up coding/extending image analysis in Python.
Language: Python - Size: 32.1 MB - Last synced at: about 1 month ago - Pushed at: about 2 months ago - Stars: 32 - Forks: 1
stardist/stardist-napari
StarDist plugin for napari
Language: Python - Size: 1.69 MB - Last synced at: about 1 month ago - Pushed at: 9 months ago - Stars: 38 - Forks: 11
chanzuckerberg/napari-hub
Discover, install, and share napari plugins
Language: TypeScript - Size: 8.48 MB - Last synced at: about 1 month ago - Pushed at: about 2 months ago - Stars: 51 - Forks: 18
samthiele/napari-hippo
A large and somewhat ugly plugin for viewing and analysing hyperspectral data in Napari
Language: Python - Size: 11.9 MB - Last synced at: about 1 month ago - Pushed at: 3 months ago - Stars: 6 - Forks: 2
napari/npe2
napari plugin engine v2
Language: Python - Size: 612 KB - Last synced at: 6 days ago - Pushed at: 7 days ago - Stars: 13 - Forks: 29
napari/napari-animation
A napari plugin for making animations
Language: Python - Size: 1.1 MB - Last synced at: 4 days ago - Pushed at: 8 months ago - Stars: 84 - Forks: 26
miura/Yodosha-BIASBook2025
『型で実践する生物画像解析 ImageJ・Python・napari』サポートサイト
Language: Jupyter Notebook - Size: 51.1 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0
MouseLand/cellpose-napari
napari plugin for cellpose (see www.cellpose.org) - an anatomical segmentation tool
Language: Python - Size: 6.89 MB - Last synced at: 6 days ago - Pushed at: 7 months ago - Stars: 52 - Forks: 24
TileDB-Inc/napari-tiledb-bioimg
TileDB BioImaging plugin for Napari
Language: Python - Size: 17.4 MB - Last synced at: about 1 month ago - Pushed at: 3 months ago - Stars: 9 - Forks: 0
hanjinliu/napari-filaments
A napari plugin for filament analysis
Language: Python - Size: 611 KB - Last synced at: about 1 month ago - Pushed at: over 1 year ago - Stars: 9 - Forks: 1
lowe-lab-ucl/arboretum
Track and lineage visualization with btrack and Napari :evergreen_tree:
Language: Python - Size: 15.2 MB - Last synced at: 29 days ago - Pushed at: 7 months ago - Stars: 45 - Forks: 11
hanjinliu/napari-text-layer
Text layer for bio-image annotation.
Language: Python - Size: 3.47 MB - Last synced at: 5 days ago - Pushed at: over 3 years ago - Stars: 7 - Forks: 2
AllenCellModeling/napari-aicsimageio
Multiple file format reading directly into napari using pure Python
Language: Python - Size: 54.8 MB - Last synced at: 6 days ago - Pushed at: 10 months ago - Stars: 35 - Forks: 10
Chris-N-K/napari-time-series-plotter
A napari Plugin for visualisaton of pixel values over time (t+ nD) as graphs.
Language: Python - Size: 32.2 MB - Last synced at: 24 days ago - Pushed at: about 1 year ago - Stars: 11 - Forks: 5
brainglobe/cellfinder-napari 📦
Efficient cell detection in large images using cellfinder in napari
Language: Python - Size: 34.3 MB - Last synced at: 14 days ago - Pushed at: over 1 year ago - Stars: 23 - Forks: 6
TheJacksonLaboratory/intro-napari-workshop
Intro to napari Workshop
Size: 27.8 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 1 - Forks: 2
InsightSoftwareConsortium/napari-itk-io
File IO with itk for napari.
Language: Python - Size: 42 KB - Last synced at: 5 days ago - Pushed at: 6 months ago - Stars: 7 - Forks: 3
BrancoLab/imgreg2D
2D image registration in python, using napari.
Language: Python - Size: 5.28 MB - Last synced at: 1 day ago - Pushed at: over 3 years ago - Stars: 16 - Forks: 3
danionella/napari-pyav
PyAV-based video reader plugin for Napari
Language: Python - Size: 43.9 KB - Last synced at: 3 months ago - Pushed at: 7 months ago - Stars: 3 - Forks: 1
SuperElastix/elastix-napari
A napari plugin for itk-elastix
Language: Python - Size: 158 KB - Last synced at: 24 days ago - Pushed at: 11 months ago - Stars: 38 - Forks: 8
FabrizioMusacchio/Napari_Bioimage_Analysis
Image data and Python scripts for the course on Bioimage analysis with Napari
Language: Python - Size: 46.4 MB - Last synced at: 2 months ago - Pushed at: almost 2 years ago - Stars: 3 - Forks: 0
GuignardLab/napari-sc3D-viewer
A plugin to visualise 3D spatial single cell omics
Language: Python - Size: 38.4 MB - Last synced at: 9 months ago - Pushed at: about 1 year ago - Stars: 21 - Forks: 2
EPFL-Center-for-Imaging/napari-imaging-epfl-2023
Image analysis with Python and Napari.
Language: Jupyter Notebook - Size: 51.5 MB - Last synced at: 3 months ago - Pushed at: over 1 year ago - Stars: 5 - Forks: 0
marx-alex/napari-bleach-correct
Napari Photobleach Correction
Language: Python - Size: 3.32 MB - Last synced at: about 1 month ago - Pushed at: over 2 years ago - Stars: 4 - Forks: 0
arkitektio-apps/mikro-napari
napari within the mikro environment
Language: Python - Size: 1.04 MB - Last synced at: 23 days ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0
alexisjapas/napari-vesicles-segmentation 📦
A simple plugin to detect vesicles in cells images.
Language: Python - Size: 1.19 MB - Last synced at: about 1 month ago - Pushed at: almost 3 years ago - Stars: 5 - Forks: 0
AllenCell/napari-allencell-segmenter
A plugin that enables image segmentation provided by Allen Institute for Cell Science
Language: Python - Size: 841 KB - Last synced at: 9 months ago - Pushed at: over 1 year ago - Stars: 16 - Forks: 6
hanjinliu/napari-macrokit
Executable script generation for napari plugins
Language: Python - Size: 2.9 MB - Last synced at: 18 days ago - Pushed at: over 2 years ago - Stars: 3 - Forks: 1
HelmholtzAI-Consultants-Munich/Automatic-Cell-Counter
A GUI based on napari for counting cells automatically in cell migration experiments
Language: Python - Size: 47.2 MB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 37 - Forks: 10
clintyr/bio-image-analysis
Example workflows for image processing, segmentation and analysis. Stitching and alignment functions also implemented.
Language: Jupyter Notebook - Size: 47.2 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0
psobolewskiPhD/JAX_NEBioimaging_napari_community_slides
Slides for a presentation about contributing to the napari community
Language: HTML - Size: 10.8 MB - Last synced at: about 2 months ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0
adrtsc/napari-blob-detection
napari plugin for blob detection in images
Language: Python - Size: 222 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 5 - Forks: 4
natelharrison/napari-live-timelapse-script
A python script to automatically load multi-channel live timelapse images into Napari.
Language: Python - Size: 517 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0
hereariim/napari-caphid
Napari-caphid was developed for updating table of quantitative data from images. Napari-caphid was developed by Imhorphen Team ( 🇫🇷 french team of University of Angers and INRAe Angers) for ECLECTIC Team (french team of University of Paris-Saclay and CNRS).
Language: Python - Size: 18.6 KB - Last synced at: 9 months ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0
pranjaldhole/napari-labelling-assistant
A lightweight plugin for visualizing labelling statistics.
Language: Python - Size: 52.7 KB - Last synced at: about 1 month ago - Pushed at: almost 3 years ago - Stars: 1 - Forks: 2
Tgnink/mfspine
dendritic spine annotation plugin for fluorescent microscopy and training scripts
Language: Jupyter Notebook - Size: 18.1 MB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0
Nadalyn-CZI/introduction-to-github
Used to complete github tutorial: https://github.com/skills/introduction-to-github
Size: 539 KB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0
rezaakb/napari-seedseg
A simple interactive segmentation plugin for napari.
Language: Python - Size: 73.2 KB - Last synced at: 3 days ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 0
BiAPoL/Quantitative_Bio_Image_Analysis_with_Python_2022
This repository hosts notebooks, information and data for the Quantitative Bio-Image Analysis with Python Course 2022.
Language: Shell - Size: 317 MB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 13 - Forks: 2
hanjinliu/napari-result-stack
Widgets and type annotations for storing function results of any types
Language: Python - Size: 1.36 MB - Last synced at: 5 days ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0
bhoeckendorf/napari-monailabel
MONAI Label client plugin for napari
Language: Python - Size: 307 KB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 4 - Forks: 0
hanjinliu/napari-multitask
Multitasking on napari
Language: Python - Size: 2.73 MB - Last synced at: 21 days ago - Pushed at: over 3 years ago - Stars: 2 - Forks: 2
EdgarLefevre/napari-deepmeta
Segment mouse lungs and metastasis on MRI images.
Language: Python - Size: 19.5 MB - Last synced at: 18 days ago - Pushed at: almost 3 years ago - Stars: 2 - Forks: 2
InsightSoftwareConsortium/itk-napari-conversion
Convert between itk and napari data structures.
Language: Python - Size: 40 KB - Last synced at: 5 days ago - Pushed at: almost 4 years ago - Stars: 3 - Forks: 0
lowe-lab-ucl/napari-btrack
Napari plugin for btrack
Language: Python - Size: 136 KB - Last synced at: about 2 years ago - Pushed at: about 2 years ago - Stars: 1 - Forks: 3
chan-labsite/PCNAdeep-napari
Visualise pcnaDeep single-cell tracking data
Language: Python - Size: 748 KB - Last synced at: about 2 years ago - Pushed at: over 3 years ago - Stars: 2 - Forks: 2
SaradhaVenkatachalapathy/annotate_images
Interactively generate/edit segmentation labels using napari
Language: Python - Size: 157 KB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 1
