Dresden
This is a collection of plugins developed by people at research institutes in Dresden, Germany: The University of Technology, TU Dresden (TUD), the Max Planck Institute for Molecular Cell Biology and Genetics (MPI-CBG) and the Center for Systems Biology Dresden (CSBD)
Robert HaaseImage Data Scientist,DFG Cluster of Excellence "Physics of Life", TU Dresden
Collection last updated: 09 July 2022
stardist-napari
stardist-napariObject Detection with Star-convex Shapes
Uwe Schmidt, Martin Weigert
Nuclei segmentation
napari-time-slicer
napari-time-slicerA meta plugin for processing timelapse data in napari timepoint by timepoint
Robert Haase
Process time-lapse data
devbio-napari
devbio-napariA bundle of napari plugins useful for 3D+t image processing and analysis for studying developmental biology.
Robert Haase
Tools for developmental biologists
beetlesafari
beetlesafariA napari plugin for loading and working with light sheet imaging data of developing embryos acquired using ClearControl, e.g. _Tribolium castaneum_.
Robert Haase
Load image data from ClearControl microscopes at CSBD
napari-process-points-and-surfaces
napari-process-points-and-surfacesProcess and analyze surfaces using open3d and vedo in napari
Robert Haase, Johannes Soltwedel
Process point and surface data
napari-stress
napari-stressInteractive surface analysis in napari for measuring mechanical stresses in biological tissues
Johannes Soltwedel, Ben J. Gross, Elijah Shelton, Carlos Gomez, Otger Campas
Measure mechanical stresses on surfaces
napari-assistant
napari-assistantA pocket calculator like interface to image processing in napari
Robert Haase, Ryan Savill
Combine image processing operations to workflows
napari-clusters-plotter
napari-clusters-plotterA plugin to use with napari for clustering objects according to their properties
Laura Zigutyte, Ryan Savill, Johannes Müller, Marcelo Zoccoler, Robert Haase
Clustering objects according to their propertie
napari-layer-details-display
napari-layer-details-displayA display for layer information and properties
Robert Haase
Visualize layer details such as shape, data type, meta data
napari-accelerated-pixel-and-object-classification
napari-accelerated-pixel-and-object-classificationPixel and label classification using OpenCL-based Random Forest Classifiers
Robert Haase
Interactive pixel and object classification using random forest classifiers
napari-pyclesperanto-assistant
napari-pyclesperanto-assistantGPU-accelerated image processing in napari using OpenCL
Robert Haase, Talley Lambert
GPU-accelerated general purpose image processing and measure properties of labeled regions
napari-simpleitk-image-processing
napari-simpleitk-image-processingProcess and analyze images using SimpleITK in napari
Robert Haase
General purpose image processing and measure properties of labeled regions
napari-skimage-regionprops
napari-skimage-regionpropsA regionprops table widget plugin for napari
Marcelo Zoccoler, Robert Haase
Measure properties of labeled regions
the-segmentation-game
the-segmentation-gameGamified image segmentation quality estimation
Robert Haase, Martin Schätz
Gamified image segmentation quality measurement
napari-apr-viewer
napari-apr-viewerA simple plugin to view APR images in napari
Joel Jonsson
Visualize adaptive particle representation files
napari-stl-exporter
napari-stl-exporterExports label images to 3D-printable stl files.
Johannes Müller
Save surfaces as STL files
napari-workflow-inspector
napari-workflow-inspectorInspect relationships between image processing operations in active workflows in napari
Robert Haase
Visualize image processing workflows as graphs
napari-segment-blobs-and-things-with-membranes
napari-segment-blobs-and-things-with-membranesA plugin based on scikit-image for segmenting nuclei and cells based on fluorescent microscopy images with high intensity in nuclei and/or membranes
Robert Haase
General purpose image processing
napari-cupy-image-processing
napari-cupy-image-processingGPU-accelerated image processing using CUDA
Robert Haase
GPU-accelerated general purpose image processing
napari-workflow-optimizer
napari-workflow-optimizerOptimize image processing workflows in napari for segmentation quality
Robert Haase
Automatically tune parameters of workflows
napari-animated-gif-io
napari-animated-gif-ioSave 3D image stacks as animated gifs
Robert Haase
Save image stacks as animated gifs
napari METROID
napari-metroidThis napari plugin creates several regions of interest of similar area over cells in a fluorescence video (2D+time). It then gets ROIs means over time and performs signal denoising: fixes photobleaching and separates signal from noise by means of blind source separation (with or without wavelet filtering).
Marcelo Leomil Zoccoler
Measure signal changes over time in multiple regions
napari-script-editor
napari-script-editorA python script editor for napari
Robert Haase
Edit python scripts in napari
napari-brightness-contrast
napari-brightness-contrastAdvanced layer visualization options
Robert Haase
Visualization configuration
napari-crop
napari-cropCrop regions in napari manually
Robert Haase, Tim Morello, Marcelo Leomil Zoccoler, Johannes Muller
Crop regions
napari-mouse-controls
napari-mouse-controlsControl napari using a touch screen
Robert Haase
Additional tools for using the mouse
napari-curtain
napari-curtainView one image over another as curtain
Robert Haase
Visualize one image over another
napari-tabu
napari-tabuA plugin for handling multiple napari windows
Robert Haase
Handle multiple napari windows
napari-folder-browser
napari-folder-browserBrowse folders of images and open them using double-click
Robert Haase
Explore image folder contents
napari-plugin-search
napari-plugin-searchFind napari plugins
Robert Haase
Search plugins
napari-plot-profile
napari-plot-profilePlot intensity along a line and create topographical views in napari
Robert Haase, Marcelo Leomil Zoccoler
Plot intensity along a line
natari
natariNapari gaming
Robert Haase
Games
napari-kics
napari-kicsA plugin to estimate chromosome sizes from karyotype images.
Alexandr Dibrov
Estimate chromosome sizes from karyotype images
Guanine Crystal Analysis
guanine-crystal-analysisA plugin for the guanine crystal segmentation, classification and characterization in the zebrafish eye
Mara Lampert
A plugin for the guanine crystal segmentation, classification and characterization in the zebrafish...