Package: devbio-napari
devbio-napariA bundle of napari plugins useful for 3D+t image processing and analysis for studying developmental biology.accelerated-pixel-and-object-classificationInstance segmentationSemantic segmentationObject classificationRandom Forest Classifier traininganimationVisualizationblob-detectionDetectionbrightness-contrastVisualizationclusters-plotterVisualizationPlottingSemantic object segmentationDimensionality reductionUnsupervised machine learningcropTransformationcurtainVisualizationczifile2File input/outputfolder-browserFile input/outputlayer-details-displayVisualizationmouse-controlsInteractionPlatyMatchImage registrationplot-profileVisualizationQuantificationplugin-searchInteractionpyclesperanto-assistantFilteringInstance segmentationSemantic segmentationQuantificationpystackregImage registrationMotion correctionRedLionfishDeconvolutionProcessingroiManual segmentationsegment-blobs-and-things-with-membranesFilteringInstance segmentationSemantic segmentationsimpleitk-image-processingFilteringInstance segmentationSemantic segmentationQuantificationskimage-regionpropsQuantificationtabuInteractionthe-segmentation-gameQuantificationSegmentation quality assuranceworkflow-inspectorVisualizationworkflow-optimizerInteractionOptimizationInstallationYou can installdevbio-naparivia conda/mamba. If you have never used conda before, pleaseread this guide first.Start by installing mamba in your base environment:conda install mamba -c conda-forgeAfterwards, create an environment using mamba.mamba create --name devbio-napari-env python=3.9 devbio-napari -c conda-forge -c pytorchAfterwards, activate the environment like this:mamba activate devbio-napari-envAfterwards, run this command from the command linenapariaThis window should open. It shows theAssistantgraphical user interface.
Read more about how to use it in itsdocumentation.Troubleshooting: Graphics cards driversIn case error messages contains "ImportError: DLL load failed while importing cl: The specified procedure could not be found"see alsoor ""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 driversNVidia driversIntel GPU driversIntel CPU OpenCL driversMicrosoft Windows OpenCL supportSometimes, mac-users need to install this:conda install -c conda-forge ocl_icd_wrapper_appleSometimes, linux users need to install this:conda install -c conda-forge ocl-icd-systemIn case installation didn't work in the first attempt, you may have to call this command line to reset the napari configuration:napari --resetTroubleshooting: pytorchIn case pytorch-related plugins fail, install pytorch as explained onits website. Consider replacingcondawithmambain 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 nvidiaOr if not:mamba install pytorch torchvision torchaudio cpuonly -c pytorchContributingContributions are very welcome.
If you want tosuggest a new napari pluginto 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.LicenseDistributed under the terms of theBSD-3license,
"devbio-napari" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.