Awesome napari-plugins that are not on the napari-hub (yet)

This is a curated list of napari plugins, that are open-source but not on the napari-hub just (yet). The intention of this list is to guide developers and users who want to find out if certain plugins exist already and/or are under development. Many of these plugins are under active development and thus, not available via pypi and the napari-hub yet. Some other plugins were decommissioned and are no longer developed. This list provides links to these valuable resources so that others can learn from the code, resurrect useful functionality and don't have to start from scratch. Another intention is to motivate developers to work together on plugins and contribute to active projects, instead of developing similar plugins in parallel.

Contributions to the list are very welcome. If you want to add an entry to this list or modify a description or link for example, please modify the list.csv file in a fork of this repository and send a pull-request. If you are new to pull-requests, you may be interested in this blog post.

The list is sorted alphabetically.

napari-annotation-project

Create projects in napari to annotate series of images and export annotations

napari-blob-detection

napari plugin for blob detection in images

napari-btrack

Napari plugin for btrack

caiman-napari-prototype

This plugin interfaces with CaImAn CNMF using QProcess and displays the spatial components using napari.layers.shapes.

napari-cistem

A napari plugin to inspect data within a cisTEM project

napari-convpaint

Segment images by pixel classification based on pre-trained convolutional layer feature extraction

napari-detectron2

napari plugin for detectron2

feature-dashboard

A ptable plotting library

napari-feature-visualization

Visualizing feature measurements on label images in napari

napari-griottes

meshes between neighbors

guanine-crystal-analysis

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

napari-hdf5-hts

simple napari plugin to view multi-well images in HDF5 format

napari-hsafm-browser

a napari plugin for viewing high-speed AFM movies

napari-idr

Napari plugin for opening images from idr.openmicroscopy.org

napari-ijroi-reader

Reader for ImageJ ROI files

napari-ilastik

ilastik plugin for napari

iterseg

napari plugin for iteratively improving 3D instance segmentation of cells (u-net x watershed)

napari-labeling

handling overlapping labels

napari-labeller

A plugin for doing manual instance segmentation.

napari-labfill

Napari plugin for creating labels using floodfill.

napari-LF

A temporary plugin with npe2 to use with napari in the process of developing a light field imaging plugin

napari-mahotas-image-processing

Process images using mahotas from within napari (experimental just playing plugin)

napari-midi

Control napari with a USB MIDI controller

napari-minimal-plugin

minimal example plugin (training material)

napari-mm

Napari plugin to load and visualize 3D image time series saved by Map Manager

napari-morphodynamics

A napari plugin to use as interface for the morphodynamics package

napari-mosquito-bb-annotations

Napari plugin for bounding box annotations

napari-n2v

A self-supervised denoising algorithm now usable by all in napari

napari_addtional_viewport

Widget to add an additional viewport to visualize on a specific shape

napari_czann_segment

Provides segmentation with a CZANN containing an ONNX model for sematic segmentation.

napari_denoiseg

A napari plugin for self-supervised denoising and segmentation of microscopy images using the DenoiSeg method

napari_etdb

napari interface for the Caltech electron tomography database

napari_hdf5_reader

Widget for multi-scale/multi-dimensional hdf5 files

napari_jroitools

Napari plugins for reading and writing ImageJ roi files and creating image profiles.

napari_ptif_reader

Reader for multi-scale (pyramidal) TIFF files

napari_tissuemaps_interface

Widget to stream images from a TissueMAPS server

napari_xml_reader

Reader for a series of images enlisted within an XML files

napariboard-proto

Prototype implementation of napari-integrated CNN training viewer

NaparIO

Napari plugin that provide better save/load for all opened layers

napari-nibabel

A napari plugin that uses nibabel to display medical images (NIFTI1 NIFTI2 ANALYZE Philips PAR/REC MINC1 MINC2 AFNI BRIK/HEAD and MGH/MGZ.)

napari-nmr-reader

A napari plugin to read NMR spectra

napari-openpiv

particle image velocimetry

napari-openpiv

particle image velocimetry

patch-viewer

WIP: A napari plugin to view attention-based heatmaps for whole slide images

PICASSO

Development of PICASSO plugin for napari

napari-pillow-image-processing

Process images using pillow from within napari (experimental just playing plugin)

proto-skimage-widgets

Example adaptor between skimage magicgui and napari WORK IN PROGRESS

napari-pssr

A plugin for training and applying pssr

napari-pyfast-image-processing

Process images using pyfast from within napari (experimental just playing plugin)

napari-scixtracer

napari plugin for data management with sciXtracer library

napari-segmentation

napari segmentation plugin

napari-sentinel-to-zarr

Writer plugin for napari to allow saving Sentinel tiffs out to ome-zarr

napari-sentinel-zip

Plugin to allow loading of SENTINEL zips into napari directly

napari-serialcellpose

batch processing for cellpose

napari-skeleton-analysis

skeleton analysis

napari-skeleton-curator

skeleton curation plugin for napari

napari-skimage-widgets

Autogenerated napari widgets for scikit-image functions.

napari-sklearn-decomposition

matrix decomposition algorithms from sklearn.decomposition within napari.

napari-sldy

Load slidebook .sldy files into napari

napari-spatial-statistics

Analyze architecture of spatially distributed objects.

napari-split-blob-labels

An adaptive 3D brush for segmentation based on local region growing

napari-spot-detection

spot detection

napari-spot-detector

A simple napari plugin for spot detection

napari-stable-diffusion

A demo of stable diffusion in napari

napari-storm

STORM plugin

napari-threedee

A suite of 3D interactivity tools for napari

napari-timeseries-opener-plugin

Simple plugin that opens separate .tif files as a 3-dimensional layer.

napari-webcam

View images from your webcam in napari (decommissioned plugin/ archived)

napari-xarray-spatial

napari plugin providing interface to xarray-spatial functions

yt-napari

A napari plugin for reading data from yt

napari-ytschema

experimental plugin for use with the yt schema

napari-zarr-writer

Napari plugin to write zarr files