devbio-napari 0.7.0

A bundle of napari plugins useful for 3D+t image processing and analysis for studying developmental biology.

devbio-napari

A bundle of napari plugins useful for 3D+t image processing and analysis for studying developmental biology.

• accelerated-pixel-and-object-classification
  • Instance segmentation
  • Semantic segmentation
  • Object classification
  • Random Forest Classifier training
• animation
  • Visualization
• blob-detection
  • Detection
• brightness-contrast
  • Visualization
• cellpose
  • Instance segmentation
  • Deep learning
• clusters-plotter
  • Visualization
  • Plotting
  • Semantic object segmentation
  • Dimensionality reduction
  • Unsupervised machine learning
• crop
  • Transformation
• curtain
  • Visualization
• czifile2
  • File input/output
• folder-browser
  • File input/output
• layer-details-display
  • Visualization
• mouse-controls
  • Interaction
• PlatyMatch
  • Image registration
• plot-profile
  • Visualization
  • Quantification
• plugin-search
  • Interaction
• process-points-and-surfaces
  • Processing
• pyclesperanto-assistant
  • Filtering
  • Instance segmentation
  • Semantic segmentation
  • Quantification
• pystackreg
  • Image registration
  • Motion correction
• roi
  • Manual segmentation
• segment-blobs-and-things-with-membranes
  • Filtering
  • Instance segmentation
  • Semantic segmentation
• simpleitk-image-processing
  • Filtering
  • Instance segmentation
  • Semantic segmentation
  • Quantification
• skimage-regionprops
  • Quantification
• tabu
  • Interaction
• the-segmentation-game
  • Quantification
  • Segmentation quality assurance
• workflow-inspector
  • Visualization
• workflow-optimizer
  • Interaction
  • Optimization

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This napari plugin was generated with Cookiecutter using with @napari's cookiecutter-napari-plugin template.

Installation

You can install devbio-napari via conda/mamba. If you have never used conda before, please read this guide first.
Start by installing mamba in your base environment:

conda install mamba -c conda-forge

Afterwards, create the environments like above but using mamba instead of conda.

mamba create --name devbio-napari-env python=3.9 devbio-napari -c conda-forge

alternatively:

conda create --name devbio-napari-env python=3.9 devbio-napari -c conda-forge

Afterwards, activate the environment like this:

conda activate devbio-napari-env

Mac-users please also install this:

conda install -c conda-forge ocl_icd_wrapper_apple

Linux users please also install this:

conda install -c conda-forge ocl-icd-system

Afterwards, run this command from the command line

naparia

This window should open. It shows the Assistant graphical user interface. Read more about how to use it in its documentation.

Troubleshooting: Graphics cards drivers

In case error messages contains "ImportError: DLL load failed while importing cl: The specified procedure could not be found" see also or ""clGetPlatformIDs failed: PLATFORM_NOT_FOUND_KHR", please install recent drivers for your graphics card and/or OpenCL device. Select the right driver source depending on your hardware from this list:

• AMD drivers
• NVidia drivers
• Intel CPU OpenCL drivers
• Microsoft Windows OpenCL support

In case installation didn't work in the first attempt, you may have to call this command line to reset the napari configuration:

napari --reset

Contributing

Contributions are very welcome. If you want to suggest a new napari plugin to become part of this distribution, please make sure it interoperates nicely with the other plugins. For example, if the plugin you suggest provided cell segmentation algorithms, please check if the resulting segmented cells can be analysed using napari-skimage-regionprops. Furthermore, please make sure the README of the plugin you are proposing comes with user documentation, e.g. a step-by-step guide with screenshots explaining what users can do with the plugin and how to use it. It is recommended to provide example data as well so that end-users can try out the plugin under conditions it was developed for.

License

Distributed under the terms of the BSD-3 license, "devbio-napari" is free and open source software

Issues

If you encounter any problems, please file an issue along with a detailed description.