BiAPoL/napari-clusters-plotter

A napari plugin for clustering objects according to their properties.

Language: Jupyter Notebook - Size: 133 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 84 - Forks: 10

scverse/napari-spatialdata

Interactive visualization of spatial omics data

Language: Python - Size: 45.4 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 55 - Forks: 18

chanzuckerberg/napari-hub

Discover, install, and share napari plugins

Language: TypeScript - Size: 8.48 MB - Last synced at: 26 days ago - Pushed at: about 1 month ago - Stars: 51 - Forks: 18

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: 5 days ago - Pushed at: 5 days ago - Stars: 50 - Forks: 13

haesleinhuepf/devbio-napari

Language: Python - Size: 1.65 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 49 - Forks: 14

haesleinhuepf/napari-accelerated-pixel-and-object-classification

GPU-accelerated, OpenCL-based Random Forest Classifiers for pixel and labeled object classification in napari.

Language: Python - Size: 47.7 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 43 - Forks: 8

matplotlib/napari-matplotlib

Linking napari layers with Matplotlib plots

Language: Python - Size: 9.1 MB - Last synced at: about 19 hours ago - Pushed at: about 20 hours ago - Stars: 40 - Forks: 22

stardist/stardist-napari

StarDist plugin for napari

Language: Python - Size: 1.69 MB - Last synced at: 26 days ago - Pushed at: 9 months ago - Stars: 38 - Forks: 11

SuperElastix/elastix-napari

A napari plugin for itk-elastix

Language: Python - Size: 158 KB - Last synced at: 18 days ago - Pushed at: 11 months ago - Stars: 38 - Forks: 8

tlambert03/napari-omero

Browse your OMERO database from within napari.

Language: Python - Size: 9.66 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 36 - Forks: 14

clEsperanto/napari_pyclesperanto_assistant

GPU-accelerated general purpose image processing and image analysis in napari

Language: Python - Size: 116 MB - Last synced at: about 7 hours ago - Pushed at: 5 days ago - Stars: 35 - Forks: 9

ome/napari-ome-zarr

A napari plugin for zarr backed OME-NGFF images

Language: Python - Size: 130 KB - Last synced at: 6 days ago - Pushed at: about 1 month ago - Stars: 33 - Forks: 22

haesleinhuepf/napari-segment-blobs-and-things-with-membranes

A plugin based on scikit-image for segmenting nuclei and cells based on fluorescent microscopy images with high intensity in nuclei and/or membranes.

Language: Python - Size: 7.69 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 26 - Forks: 8

haesleinhuepf/napari-process-points-and-surfaces

Process and analyze surfaces using vedo in napari.

Language: Python - Size: 185 MB - Last synced at: 22 days ago - Pushed at: 12 months ago - Stars: 23 - Forks: 4

brainglobe/cellfinder-napari 📦

Efficient cell detection in large images using cellfinder in napari

Language: Python - Size: 34.3 MB - Last synced at: 8 days ago - Pushed at: over 1 year ago - Stars: 23 - Forks: 6

volume-em/empanada-napari

Panoptic segmentation algorithms for 2D and 3D electron microscopy in napari

Language: Python - Size: 8.22 MB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 22 - Forks: 9

haesleinhuepf/napari-cupy-image-processing

Language: Python - Size: 10.3 MB - Last synced at: 6 days ago - Pushed at: over 1 year ago - Stars: 22 - 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

haesleinhuepf/napari-simpleitk-image-processing

Process images using SimpleITK in napari

Language: Python - Size: 8.49 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 20 - Forks: 4

haesleinhuepf/napari-plot-profile

Language: Python - Size: 14.1 MB - Last synced at: 6 days ago - Pushed at: 21 days ago - Stars: 17 - Forks: 5

LIDS-UNICAMP/grabber

Grabber: A Tool to Improve Convergence in Interactive Image Segmentation

Language: Python - Size: 31.4 MB - Last synced at: 17 days ago - Pushed at: about 2 years ago - Stars: 17 - Forks: 2

haesleinhuepf/napari-workflow-optimizer

Optimize image processing workflows in napari

Language: Python - Size: 28 MB - Last synced at: 6 days ago - Pushed at: almost 3 years ago - Stars: 17 - Forks: 2

haesleinhuepf/natari

Napari gaming

Language: Python - Size: 46.9 MB - Last synced at: 6 days ago - Pushed at: over 3 years ago - Stars: 17 - 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: 8 months ago - Pushed at: over 1 year ago - Stars: 16 - Forks: 6

brainglobe/brainglobe-napari-io

Read and write files from the BrainGlobe neuroanatomy suite

Language: Python - Size: 25.5 MB - Last synced at: about 18 hours ago - Pushed at: about 19 hours ago - Stars: 14 - Forks: 5

multiview-stitcher/napari-stitcher

A napari plugin for stitching large multi-positioning datasets in 2/3D+t using multiview-stitcher

Language: Python - Size: 23.9 MB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 14 - Forks: 4

ilastik/ilastik-napari

ilastik plugin for napari

Language: Python - Size: 2.58 MB - Last synced at: 6 days ago - Pushed at: about 1 year ago - Stars: 14 - Forks: 3

PolusAI/bfio

Interface to the Bioformats Java library

Language: Python - Size: 60.5 MB - Last synced at: 16 days ago - Pushed at: 4 months ago - Stars: 13 - Forks: 8

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

haesleinhuepf/napari-brightness-contrast

Language: Python - Size: 46.7 MB - Last synced at: 6 days ago - Pushed at: over 2 years ago - Stars: 13 - Forks: 4

janclemenslab/napari-video

Napari plugin for working with video files.

Language: Jupyter Notebook - Size: 27.3 KB - Last synced at: 9 days ago - Pushed at: 7 months ago - Stars: 12 - Forks: 3

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: 18 days ago - Pushed at: about 1 year ago - Stars: 11 - Forks: 5

haesleinhuepf/napari-script-editor

A python script editor plugin for napari

Language: Python - Size: 34.7 MB - Last synced at: 6 days ago - Pushed at: almost 2 years ago - Stars: 11 - Forks: 0

junlabucsd/napari-mm3

Mother machine image analysis through napari

Language: Jupyter Notebook - Size: 20.1 MB - Last synced at: about 1 month ago - Pushed at: 3 months ago - Stars: 10 - Forks: 4

BiAPoL/napari-crop

Language: Jupyter Notebook - Size: 34.1 MB - Last synced at: 29 days ago - Pushed at: 29 days ago - Stars: 9 - Forks: 4

TileDB-Inc/napari-tiledb-bioimg

TileDB BioImaging plugin for Napari

Language: Python - Size: 17.4 MB - Last synced at: 26 days ago - Pushed at: 3 months ago - Stars: 9 - Forks: 0

PolarizedLightFieldMicroscopy/napari-LF

Light field imaging plugin for napari

Language: Python - Size: 103 MB - Last synced at: 19 days ago - Pushed at: 6 months ago - Stars: 9 - Forks: 3

gatoniel/napari-3d-ortho-viewer

Napari 3D Ortho Viewer - an ortho viewer for napari for 3D images

Language: Python - Size: 2.68 MB - Last synced at: 21 days ago - Pushed at: over 1 year ago - Stars: 9 - Forks: 2

haesleinhuepf/napari-blender-bridge

Transfer surface layers between Napari and Blender.

Language: Python - Size: 13.4 MB - Last synced at: 6 days ago - Pushed at: about 2 years ago - Stars: 8 - Forks: 1

haesleinhuepf/napari-workflow-inspector

Inspect relationships between napari-plugins in active workflows.

Language: Python - Size: 1020 KB - Last synced at: 6 days ago - Pushed at: almost 3 years ago - Stars: 8 - Forks: 4

InsightSoftwareConsortium/napari-itk-io

File IO with itk for napari.

Language: Python - Size: 42 KB - Last synced at: 8 days ago - Pushed at: 6 months ago - Stars: 7 - Forks: 3

sylvainprigent/napari-stracking

Napari plugin for particles tracking

Language: Python - Size: 70.2 MB - Last synced at: 22 days ago - Pushed at: 11 months ago - Stars: 7 - Forks: 5

haesleinhuepf/napari-folder-browser

Language: Python - Size: 9.28 MB - Last synced at: 6 days ago - Pushed at: about 1 year ago - Stars: 7 - Forks: 2

rdemets/napari-yolov5

Language: Python - Size: 94.5 MB - Last synced at: about 1 month ago - Pushed at: over 2 years ago - Stars: 7 - Forks: 1

sylvainprigent/napari-tracks-reader

napari reader plugin for tracking

Language: Python - Size: 295 KB - Last synced at: about 17 hours ago - Pushed at: over 3 years ago - Stars: 7 - Forks: 2

MBPhys/napari-medical-image-formats

A napari plugin in order to read and write medical image formats such as DICOM, DICOM Series and NIfTI

Language: Python - Size: 21.5 KB - Last synced at: 11 days ago - Pushed at: over 3 years ago - Stars: 7 - Forks: 0

hanjinliu/napari-text-layer

Text layer for bio-image annotation.

Language: Python - Size: 3.47 MB - Last synced at: about 1 month ago - Pushed at: over 3 years ago - Stars: 7 - Forks: 2

brainglobe/napari-brainreg-standard 📦

Visualise brainreg registration output in standard space

Language: Python - Size: 13.5 MB - Last synced at: 13 days ago - Pushed at: over 4 years ago - Stars: 7 - Forks: 0

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: 26 days ago - Pushed at: 2 months ago - Stars: 6 - Forks: 2

haesleinhuepf/napari-laptrack

Tracking particles in Napari, using the LapTrack library

Language: Python - Size: 8.59 MB - Last synced at: 6 days ago - Pushed at: almost 2 years ago - Stars: 6 - Forks: 1

mpicbg-csbd/napari-kics

A plugin to estimate chromosome sizes from karyotype images.

Language: Python - Size: 8.15 MB - Last synced at: 7 months ago - Pushed at: almost 3 years ago - Stars: 6 - Forks: 0

hiroalchem/napari-labelimg4classification

A simple image-level annotation tool supporting multi-channel images for napari.

Language: Python - Size: 7.75 MB - Last synced at: about 1 month ago - Pushed at: over 3 years ago - Stars: 6 - Forks: 2

haesleinhuepf/napari-time-slicer

A meta plugin for processing timelapse data timepoint by timepoint in napari

Language: Python - Size: 36.1 MB - Last synced at: 6 days ago - Pushed at: over 1 year ago - Stars: 5 - Forks: 3

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

haesleinhuepf/napari-animated-gif-io

Open and save 3D image stacks as animated gifs in napari

Language: Python - Size: 6.57 MB - Last synced at: 6 days ago - Pushed at: about 2 years ago - Stars: 5 - Forks: 2

alexisjapas/napari-vesicles-segmentation 📦

A simple plugin to detect vesicles in cells images.

Language: Python - Size: 1.19 MB - Last synced at: 25 days ago - Pushed at: almost 3 years ago - Stars: 5 - Forks: 0

MercaderLabAnatomy/napari-tmidas

Batch processing of microscopy image data in Napari

Language: Python - Size: 218 KB - Last synced at: 13 days ago - Pushed at: 13 days ago - Stars: 4 - Forks: 0

CAREamics/careamics-napari

napari plugin for CAREamics

Language: Python - Size: 228 KB - Last synced at: 21 days ago - Pushed at: 21 days ago - Stars: 4 - Forks: 2

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

marx-alex/napari-bleach-correct

Napari Photobleach Correction

Language: Python - Size: 3.32 MB - Last synced at: 26 days ago - Pushed at: over 2 years ago - Stars: 4 - Forks: 0

haesleinhuepf/napari-curtain

Language: Python - Size: 3.8 MB - Last synced at: 6 days ago - Pushed at: over 3 years ago - Stars: 4 - Forks: 1

brainglobe/napari-brainreg 📦

Visualise brainreg registration output

Language: Python - Size: 19.3 MB - Last synced at: about 2 years ago - Pushed at: over 3 years ago - Stars: 4 - Forks: 0

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: 2 days ago - Pushed at: about 1 month ago - Stars: 3 - Forks: 1

jhnnsrs/faser

A python based toolkit for psf estimation using a vectorial model of the electromagnetic field

Language: Python - Size: 16.3 MB - Last synced at: 3 days ago - Pushed at: 4 months ago - Stars: 3 - Forks: 0

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

hereariim/napari-aphid

This directory contains all the elements and structure of the napari-aphid plugin

Language: Python - Size: 265 MB - Last synced at: 6 months ago - Pushed at: almost 2 years ago - Stars: 3 - Forks: 0

haesleinhuepf/napari-layer-details-display

Language: Python - Size: 261 KB - Last synced at: 6 days ago - Pushed at: about 2 years ago - Stars: 3 - Forks: 1

hanjinliu/napari-macrokit

Executable script generation for napari plugins

Language: Python - Size: 2.9 MB - Last synced at: 12 days ago - Pushed at: over 2 years ago - Stars: 3 - Forks: 1

czbiohub/napari-mosquito-bb-annotations

Napari plugin for bounding box annotations

Language: Python - Size: 7.43 MB - Last synced at: about 2 years ago - Pushed at: about 3 years ago - Stars: 3 - Forks: 0

MBPhys/Partial-Aligner

Partial-Aligner is a napari plugin used for manual registration and histology slide repair

Language: Python - Size: 2.33 MB - Last synced at: about 2 years ago - Pushed at: over 3 years ago - Stars: 3 - Forks: 0

InsightSoftwareConsortium/itk-napari-conversion

Convert between itk and napari data structures.

Language: Python - Size: 40 KB - Last synced at: 8 days ago - Pushed at: almost 4 years ago - Stars: 3 - Forks: 0

super-resolution/napari-locan

Napari plugin to use locan methods in napari

Language: Python - Size: 4.74 MB - Last synced at: 9 days ago - Pushed at: about 1 month ago - Stars: 2 - Forks: 0

bwmr/napari-segselect

Napari Plugin to clean membrain-seg segmentations

Language: Python - Size: 678 KB - Last synced at: 21 days ago - Pushed at: 3 months ago - Stars: 2 - Forks: 0

palvarezc/cavendish-particle-tracks

A Napari plugin to perform a simple particle tracking analysis for the Cavendish laboratory's Undergraduate Part II Particle Tracks experiment.

Language: Python - Size: 90.1 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 2 - Forks: 0

MontpellierRessourcesImagerie/napari-J

Connect Napari with FIJI/ImageJ

Language: Python - Size: 130 KB - Last synced at: 21 days ago - Pushed at: 9 months ago - Stars: 2 - Forks: 2

EPFL-Center-for-Imaging/napari-rembg

AI-based image segmentation in Napari.

Language: Python - Size: 54.6 MB - Last synced at: 9 days ago - Pushed at: about 1 year ago - Stars: 2 - Forks: 0

EPFL-Center-for-Imaging/napari-orientationpy

Analyze orientations in 2D, 3D, and RGB images in Napari.

Language: Python - Size: 9.54 MB - Last synced at: 15 days ago - Pushed at: over 1 year ago - Stars: 2 - Forks: 0

EPFL-Center-for-Imaging/napari-magic-wand

"Magic wand" annotation in Napari.

Language: Python - Size: 26.2 MB - Last synced at: 14 days ago - Pushed at: over 1 year ago - Stars: 2 - Forks: 0

hereariim/napari-pixel-correction

This directory contains the files that make up the napari-pixel-correction module. This module is used to annotate the segmentation masks.

Language: Python - Size: 5.11 MB - Last synced at: 18 days ago - Pushed at: over 1 year ago - Stars: 2 - Forks: 0

BiAPoL/guanine-crystal-analysis

A plugin for the guanine crystal segmentation, classification and characterization in the zebrafish eye

Language: Cool - Size: 6.44 MB - Last synced at: 11 days ago - Pushed at: almost 2 years ago - Stars: 2 - Forks: 0

mesoSPIM/mesoSPIM-lazy-loader

Lazy loader napari plugin for mesoSPIM datasets

Language: Python - Size: 1.38 MB - Last synced at: almost 2 years ago - Pushed at: about 2 years ago - Stars: 2 - Forks: 0

EdgarLefevre/napari-deepmeta

Segment mouse lungs and metastasis on MRI images.

Language: Python - Size: 19.5 MB - Last synced at: 12 days ago - Pushed at: almost 3 years ago - Stars: 2 - Forks: 2

bhoeckendorf/napari-remote-interaction

Remotely interacts with napari

Language: Python - Size: 29.3 KB - Last synced at: about 2 years ago - Pushed at: over 3 years ago - Stars: 2 - Forks: 0

hanjinliu/napari-multitask

Multitasking on napari

Language: Python - Size: 2.73 MB - Last synced at: 15 days ago - Pushed at: over 3 years ago - Stars: 2 - Forks: 2

DragaDoncila/napari-sentinel-zip

Plugin to allow loading of SENTINEL zips into napari directly

Language: Python - Size: 5.44 MB - Last synced at: 26 days ago - Pushed at: over 4 years ago - Stars: 2 - Forks: 0

haesleinhuepf/napari-mouse-controls

Control zoom, slicing and contrast windowing with mouse and touch screen

Language: Python - Size: 12 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 1 - Forks: 2

wisstock/domb-napari

napari plugin for analyzing fluorescence-labeled proteins redistribution

Language: Python - Size: 20.5 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 1 - Forks: 0

EPFL-Center-for-Imaging/napari-z-plotter

Interactively plot the image intensity along the depth axis of a 3D image dataset.

Language: Python - Size: 2.61 MB - Last synced at: 9 days ago - Pushed at: 12 months ago - Stars: 1 - Forks: 1

EPFL-Center-for-Imaging/napari-floodfill

Interactive object annotation in Napari using a flood fill tool.

Language: Python - Size: 8.03 MB - Last synced at: 23 days ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0

yapic/napari-hdf5-labels-io

Napari plugin to store Napari projects in a .h5 file. Label layer are stored in a sparse representation (COO list).

Language: Python - Size: 81.1 KB - Last synced at: 25 days ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 4

pranjaldhole/napari-labelling-assistant

A lightweight plugin for visualizing labelling statistics.

Language: Python - Size: 52.7 KB - Last synced at: 27 days ago - Pushed at: almost 3 years ago - Stars: 1 - Forks: 2

chili-chiu/napari-labels-overlap

napari-labels-overlap plugin

Language: Python - Size: 26.4 KB - Last synced at: 9 days ago - Pushed at: almost 3 years ago - Stars: 1 - Forks: 0

DKFZ-TMTRR/Partial-Aligner

Partial-Aligner is a napari plugin used for manual registration and histology slide repair

Language: Python - Size: 2.34 MB - Last synced at: 12 days ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 0

MBPhys/napari-elementary-numpy-operations

A napari plugin covers elementary numpy operations like swap axes, flip, sqeeze an array or rotate an arrays by 90° steps

Language: Python - Size: 7.81 KB - Last synced at: 28 days ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 1

haesleinhuepf/napari-mahotas-image-processing

Language: Python - Size: 1.25 MB - Last synced at: 11 days ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 0

MBPhys/Image-Composer

A napari plugin in order to compose a background image with a foreground image

Language: Python - Size: 13.7 KB - Last synced at: 9 days ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 0

haesleinhuepf/napari-pyfast-image-processing

Use pyFAST's CPU/GPU-accelerated image processing from within napari.

Language: Python - Size: 8.79 MB - Last synced at: 2 months ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 0

haesleinhuepf/napari-webcam 📦

Language: Python - Size: 26.4 KB - Last synced at: 29 days ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 1

brainglobe/napari-cellfinder 📦

Language: Python - Size: 8.39 MB - Last synced at: about 2 years ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 1

haesleinhuepf/napari-oclrfc

Language: Python - Size: 3.97 MB - Last synced at: 13 days ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 0