Socket
Socket
Sign inDemoInstall

devbio-napari

Package Overview
Dependencies
35
Maintainers
1
Alerts
File Explorer

Install Socket

Detect and block malicious and high-risk dependencies

Install

devbio-napari

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

    0.10.1

Maintainers
1

Readme

devbio-napari

License PyPI Python Version tests codecov Development Status napari hub

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


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 an environment using mamba.

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

Afterwards, activate the environment like this:

mamba activate devbio-napari-env

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.

img.png

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:

Sometimes, mac-users need to install this:

conda install -c conda-forge ocl_icd_wrapper_apple

Sometimes, linux users need to install this:

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

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

Troubleshooting: pytorch

In case pytorch-related plugins fail, install pytorch as explained on its website. Consider replacing conda with mamba in given instructions.

For example if you have an NVidia GPU at hand, install pytorch like this:

mamba install pytorch torchvision torchaudio pytorch-cuda=11.7 -c pytorch -c nvidia

Or if not:

mamba install pytorch torchvision torchaudio cpuonly -c pytorch

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.

FAQs


Did you know?

Socket for GitHub automatically highlights issues in each pull request and monitors the health of all your open source dependencies. Discover the contents of your packages and block harmful activity before you install or update your dependencies.

Install

Related posts

SocketSocket SOC 2 Logo

Product

  • Package Alerts
  • Integrations
  • Docs
  • Pricing
  • FAQ
  • Roadmap

Stay in touch

Get open source security insights delivered straight into your inbox.


  • Terms
  • Privacy
  • Security

Made with ⚡️ by Socket Inc