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.
Create projects in napari to annotate series of images and export annotations
napari plugin for blob detection in images
Napari plugin for btrack
This plugin interfaces with CaImAn CNMF using QProcess and displays the spatial components using napari.layers.shapes.
A napari plugin to inspect data within a cisTEM project
Segment images by pixel classification based on pre-trained convolutional layer feature extraction
napari plugin for detectron2
A ptable plotting library
Visualizing feature measurements on label images in napari
meshes between neighbors
A plugin for the guanine crystal segmentation classification and characterization in the zebrafish eye
simple napari plugin to view multi-well images in HDF5 format
a napari plugin for viewing high-speed AFM movies
Napari plugin for opening images from idr.openmicroscopy.org
Reader for ImageJ ROI files
ilastik plugin for napari
napari plugin for iteratively improving 3D instance segmentation of cells (u-net x watershed)
handling overlapping labels
A plugin for doing manual instance segmentation.
Napari plugin for creating labels using floodfill.
A temporary plugin with npe2 to use with napari in the process of developing a light field imaging plugin
Process images using mahotas from within napari (experimental just playing plugin)
Control napari with a USB MIDI controller
minimal example plugin (training material)
Napari plugin to load and visualize 3D image time series saved by Map Manager
A napari plugin to use as interface for the morphodynamics package
Napari plugin for bounding box annotations
A self-supervised denoising algorithm now usable by all in napari
Widget to add an additional viewport to visualize on a specific shape
Provides segmentation with a CZANN containing an ONNX model for sematic segmentation.
A napari plugin for self-supervised denoising and segmentation of microscopy images using the DenoiSeg method
napari interface for the Caltech electron tomography database
Widget for multi-scale/multi-dimensional hdf5 files
Napari plugins for reading and writing ImageJ roi files and creating image profiles.
Reader for multi-scale (pyramidal) TIFF files
Widget to stream images from a TissueMAPS server
Reader for a series of images enlisted within an XML files
Prototype implementation of napari-integrated CNN training viewer
Napari plugin that provide better save/load for all opened layers
A napari plugin that uses nibabel to display medical images (NIFTI1 NIFTI2 ANALYZE Philips PAR/REC MINC1 MINC2 AFNI BRIK/HEAD and MGH/MGZ.)
A napari plugin to read NMR spectra
particle image velocimetry
particle image velocimetry
WIP: A napari plugin to view attention-based heatmaps for whole slide images
Development of PICASSO plugin for napari
Process images using pillow from within napari (experimental just playing plugin)
Example adaptor between skimage magicgui and napari WORK IN PROGRESS
A plugin for training and applying pssr
Process images using pyfast from within napari (experimental just playing plugin)
napari plugin for data management with sciXtracer library
napari segmentation plugin
Writer plugin for napari to allow saving Sentinel tiffs out to ome-zarr
Plugin to allow loading of SENTINEL zips into napari directly
batch processing for cellpose
skeleton analysis
skeleton curation plugin for napari
Autogenerated napari widgets for scikit-image functions.
matrix decomposition algorithms from sklearn.decomposition within napari.
Load slidebook .sldy files into napari
Analyze architecture of spatially distributed objects.
An adaptive 3D brush for segmentation based on local region growing
spot detection
A simple napari plugin for spot detection
A demo of stable diffusion in napari
STORM plugin
A suite of 3D interactivity tools for napari
Simple plugin that opens separate .tif files as a 3-dimensional layer.
View images from your webcam in napari (decommissioned plugin/ archived)
napari plugin providing interface to xarray-spatial functions
A napari plugin for reading data from yt
experimental plugin for use with the yt schema
Napari plugin to write zarr files