Saravanan666/pypi-org huggingface dataset:
Package: napari-tiledb-bioimg
napari-tiledb-bioimgThis plugin supports reading and writing TileDB-BioImaging multi-resolution arrays within Napari.Demohttps://github.com/TileDB-Inc/napari-tiledb-bioimg/assets/327706/b408d634-6ad0-4160-8571-18cf8e37b4ccInstallation[pending PyPI release!] You can installnapari-tiledb-bioimgvia [pip]:pip install napari-tiledb-bioimgQuickstartAfteringesting data usingtiledb-bioimg, then:Local images can be loaded using Napari'sFile -> Open Folder, and selecting the TileDB array folder. Choose thenapari-tiledb-bioimgplugin, if prompted.Remote arrays (S3, TileDB Cloud) may be loaded using either thenapariCLI command:napari --plugin napari-tiledb-bioimg s3://<bucket>/<path/to/tiledb_array>... or the Napari viewer load command within the Python prompt:# Within a Napari-enabled Python/IPython prompt, run:
import napari
viewer = napari.Viewer()

viewer.open("tiledb://<namespace>/<array name or UUID>", plugin="napari-tiledb-bioimg")ContributingContributions are very welcome. Tests can be run with tox or pytest.Installation from git:pip install git+https://github.com/TileDB-Inc/napari-tiledb-bioimg.gitLicenseDistributed under the terms of the [MIT] license,
"napari-tiledb-bioimg" is free and open source software.IssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-tiler
napari-tilerN-dimensional tiling and merging support for napariThis plugin allows the user to split an image into a stack of tiles and subsequently merge the tiles to reconstruct the orignal image.
SeeTilerby@thelayfor more details.Thisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.InstallationOption 1 (recommended)You can installnapari-tilerfrom the napari plugin manager. Go toPlugins -> Install/Uninstall Package(s), then search fornapari-tiler. ClickInstall.Option 2You can also installnapari-tilerviapip:pip install napari-tilerTo install latest development version:pip install git+https://github.com/tdmorello/napari-tiler.gitQuick StartOpen a file in napari. The file may have any number of dimensions (e.g. z-stack, time series, ...)Start the plugin (Plugins -> napari-tiler: make_tiles)Select the input layer from the dropdown boxSelect parameters for tilingClickRunContributingThis project usesPoetryfor dependency management.
To set up the development environment, it is recommended to use:conda env create -f environment.yamlContributions are very welcome. Tests can be run withtox, please ensure the coverage at least stays the same before you submit a pull request.LicenseDistributed under the terms of theBSD-3license,
"napari-tiler" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-timeseries-opener-plugin
napari-timeseries-opener-pluginSimple plugin that opens separate .tif files as a 3-dimensional layer.Thisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.RunIn powershell run when you do not have sufficient GPU support in your environment$env:CUDA_VISIBLE_DEVICES=-1; napariInstallationYou can installnapari-timeseries-opener-pluginviapip:pip install napari-timeseries-opener-pluginTo install latest development version :pip install git+https://github.com/gatoniel/napari-timeseries-opener-plugin.gitContributingContributions are very welcome. Tests can be run withtox, please ensure
the coverage at least stays the same before you submit a pull request.LicenseDistributed under the terms of theBSD-3license,
"napari-timeseries-opener-plugin" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-timestamper
napari-timestamperA simple plugin to add a timestamp overlay to napari
uses some private overlay functionality, so may break in the futureThisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-timestamperviapip:pip install napari-timestamperTo install latest development version :pip install git+https://github.com/bgraedel/napari-timestamper.gitContributingContributions are very welcome. Tests can be run withtox, please ensure
the coverage at least stays the same before you submit a pull request.LicenseDistributed under the terms of theBSD-3license,
"napari-timestamper" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-tissuumaps
🏝 napari-tissuumaps 🧫A plugin to export Napari projects toTissUUmaps.This plugins adds a new writer toNaparito export projects toTissUUmaps. Exported projects can then be open on the browser or on a standalone GUI withTissUUmaps. More information and demonstrations are available on theTissUUmaps webpage.🚀 FeaturesThe plugin now supports:Exporting imagesExporting labelsExporting pointsExporting shapes, including:PolygonsRectanglesLinesPathsEllipsesThe plugin exports the right color for the points, shapes and labels and also saves the visibility/opacity of each layers. The shapes are exported in the GeoJSON format, the points in CSV files, and images as TIFFs.📺 InstallationYou can installnapari-tissuumapsviapip:pip install napari-tissuumapsYou can also installnapari-tissumapsvianapari:In Napari, access the menubar, Plugins > Install/Uninstall Plugins.
Search for napari-tissuumaps in the list and choose install, or typenapari-tissuumapsin the "install by name/url, or drop file..." text area and choose
install.⛏ UsageTo export a project for TissUUmaps, access the menubar, File > Save All Layers... and
type in a filename. Choose the.tmapextension in the dropdown and click on the Save
button, It will create a folder containing all the necessary files for TissUUmaps.👩‍💻 ContributingContributions are very welcome. Tests can be run withtox, please ensure
the coverage at least stays the same before you submit a pull request.⚖️ LicenseDistributed under the terms of theMITlicense,
"napari-tissuumaps" is free and open source software🚒 IssuesIf you encounter any problems, please [file an issue] along with a detailed description.
Package: napari-tomocube-data-viewer
napari-tomocube-data-viewerA plugin to visualize three-dimensional data fromTomocube's holotomographyThisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-tomocube-data-viewerviapiporconda:pip install napari-tomocube-data-viewer
conda install napari-tomocube-data-viewerContributingContributions are very welcome. Tests can be run withtox, please ensure
the coverage at least stays the same before you submit a pull request.LicenseDistributed under the terms of theMITlicense,
"napari-tomocube-data-viewer" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-tomodl
napari-tomodlA plugin for optical projection tomography reconstruction with model-based neural networks.Thisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.Introduction and usageToMoDL allows users to reconstruct tomography images from its raw projections juts from uploading them as an ordered stack of files into the napari viewer.1 - Load ordered stack: Click File -> Open Files as Stack... and load the angular projections for parallel beam optical tomography reconstruction.2 - Select the current volume in the dropdown menu with the button 'Select image layer'. Notice that the projections should be in grayscale and more than one slide in the stack.3 - If the axis is not correctly aligned in acquisition time, we provide an algorithm to do so by clicking on 'Align axis'. This will align the sinogram respect to the center of the detector in order to maximise the variance of the reconstructions. See Walls et al.4 - Reshape the reconstructed volume to a desired size. This can be useful to prevent exhausting your computing capabilities.5 - Clip to circle should be False by default.6 - Choose if filtering should be used. By the moment we only allow using ramp filtering for FBP only (both CPU and GPU).7 - Choose the correct order of the axis of the projections (T -> Theta axis, Q -> Detector axis)8 - Reconstruct! A new Layer should be created on top of the projections stack containing the reconstructed volume.InstallationThis package requirestorch-radonfor optimized GPU tomographic reconstruction:pip install 'torch-radon @ https://rosh-public.s3-eu-west-1.amazonaws.com/radon-v2/cuda-11.1/torch-1.8/torch_radon-2.0.0-cp38-cp38-linux_x86_64.whl'andPyTorch == 1.8.0via wheel, which can be downloaded and installed with:pip install 'torch @ https://download.pytorch.org/whl/cu111/torch-1.8.0%%2Bcu111-cp38-cp38-linux_x86_64.whl'You can installnapari-tomodlviapip:pip install napari-tomodlContributingContributions are very welcome. Tests can be run withtox, please ensure
the coverage at least stays the same before you submit a pull request.LicenseDistributed under the terms of theMITlicense,
"napari-tomodl" is free and open source softwareIssuesIf you encounter any problems, please [file an issue] along with a detailed description.
Package: napari-tomoslice
napari-tomosliceA napari plugin for visualising and interacting with electron cryotomograms.InstallationYou can installnapari-tomosliceviapip:pip install napari-tomosliceUsageThis plugin provides a user interface for opening electron cryotomograms in
napari as both volumes and slices through volumes.The plugin can be opened from thepluginsmenu in napari, or withnapari-tomosliceat the command line.Usage:napari-tomoslice [TOMOGRAM_FILE]An interactive tomogram slice viewer in napari.Controls:x/y/z - align normal vector along x/y/z axisclick and drag - shift plane along its normal vectoralt-click - add point on plane (if points layer is active)o - align plane normal to view direction[] - decrease/increase plane thicknessArguments:[TOMOGRAM_FILE]Options:--help                          Show this message and exit.ContributingContributions are very welcome.LicenseDistributed under the terms of theBSD-3license,
"napari-tomoslice" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-tomotwin
napari-tomotwinSeveral tools for the work with TomoTwin :-)InstallationYou can installnapari-tomotwinviapip:pip install napari-tomotwinLicenseDistributed under the terms of theMozilla Public License 2.0license,
"napari-tomotwin" is free and open source softwareIssuesIf you encounter any problems, please [file an issue] along with a detailed description.
Package: napari-tools-menu
napari-tools-menuAttaches a customizable Tools menu to napariUsageJust add napari-tools-menu to the dependencies of your napari-plugin. Afterwards, you can annotate your functions and dock widgets using the following syntax.
The specified menu path will be used to put your tool in the right place in the tools menu.
All menus and sub-menus will be listed alphabetically.fromnapari_tools_menuimportregister_function,register_action,register_dock_widget@register_action(menu="Utilities > Action")deftest_function(viewer):print("hello")@register_function(menu="Utilities > Function")deftest_function_with_params(sigma:float=0.5):print("sigma",sigma)@register_dock_widget(menu="Utilities > Widget")classExampleQWidget(QWidget):def__init__(self,napari_viewer):Theregister_functionandregister_dock_widgetannotations are made foranalysis functionsandgraphical user interfacesas explained in thenapari-plugin tutorial.
Theregister_actionannotation is made for functions with a single parameter: the napariviewer. This function is executed when the user clicks the menu. This might for example be useful for applying a certain operation to all currently selected layers.Note: This implementation is based on amonkey patchof napari, tested with napari 0.4.11.
Thus, it might stop working with a future version of napari, e.g. when thenew plugin engineis finished.
For now it is a nice workaround to ease the life of end-users.Menu name suggestionsTo keep the Tools menu clean and organized, some suggestions should be made.
Create category menus that classify your tool in a way such that a broad audience knows what it's doing. Examples:Filtering / noise removalFiltering / background removalFiltering / edge enhancementFiltering / deconvolutionImage mathRegistrationSegmentation / binarizationSegmentation / labelingSegmentation post-processingMeasurementVisualizationUtilitiesPut a descriptive function name in the menu name first and the implementation behind. Examples:Segmentation / Binarization > Threshold (Otsu et al 1979)Segmentation / Binarization > Threshold (my algorithm)Segmentation / Labeling > Cell labeling (CellLab)Segmentation / Labeling > Nuclei segmentation (Nuc-Seg)Example code:@register_action(menu="Segmentation > Threshold (Otsu et al 1979)")defthreshold_otsu(viewer):pass@register_action(menu="Segmentation > Threshold (my algorithm)")defmy_algorithm(viewer):pass@register_action(menu="Segmentation > Cell labeling (CellLab)")defcelllab(viewer):pass@register_action(menu="Segmentation > Nuclei segmentation (Nuc-Dect)")defnucl_dect(viewer):passThe menu would then look like this:Again, there are no constraints. However, please make the life of (y)our users easy by keeping this menu well organized.InstallationYou can installnapari-tools-menuviapip:pip install napari-tools-menuContributingContributions are very welcome. Tests can be run with [pytest], please ensure
the coverage at least stays the same before you submit a pull request.LicenseDistributed under the terms of theBSD-3license,
"napari-tools-menu" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-tracing
napari-tracingNapari Tracer PluginTheNapari Tracer Pluginprovides an intuitive interface for users to load images, perform brightest path tracing, and visualize the results. This plugin, which is built on top of the Napari viewer, enables users to explore and annotate complex images, and take advantage of the viewer's built-in features such as zooming, panning, and adjusting contrast while viewing their tracings. TheNapari Tracer Pluginuses the brightest path tracing algorithms frombrightest-path-libto provide an interactive path building process for users to create traced segments in 2D and 3D images.ExamplesYou can download our2Dand3Dexample tif files.FeaturesLoad images and trace paths in 2D and 3D.Offloads computations to a background thread to ensure a responsive user interface.Two tracing modes: disjoint and continuous. Disjoint segments refer to paths that do not share any points, while continuous segments start from the endpoint of a previously traced path.Verify traced segments and cancel tracing if necessary.Save traced paths in SWC format commonly used in biology to represent neuronal morphology.Load previously saved tracings in SWC format.InstallationYou can installnapari-tracingvia pip:pip install napari-tracingTo install latest development version :pip install git+https://github.com/mapmanager/napari-tracing.gitUsageOnce installed, the Napari Tracer Plugin can be accessed from the Napari menu under "Plugins" > "napari tracing: Tracer Widget". This will open the plugin interface, where you can load your image and start tracing.TracingTo trace a path, select the "Trace" mode and the image layer that you want to trace from their respective dropdowns.Once you select the image, a points layer called the terminal points layer will be created on the Napari viewer where you can add the start and end point.Click the "Start Tracing" button to perform brightest path tracing between the points.The traced path will appear in a new points layer called the tracing result result layer in the Napari viewer as a line overlay.Each new traced segment is verified, so you can either accept the tracing or reject it. If you choose to reject the tracing, you can try again with a different set of points if necessary.You can click on the "Cancel Tracing" button to cancel a tracing that is in progress.Saving and loading tracingsTo save a tracing, click on the "Save Trace" button from the plugin menu. This will save the traced path in SWC format to a file of your choosing.To load a previously saved tracing, click on the "Load Trace" button and choose the SWC file you want to load. The traced path will appear in the Napari viewer.ContributingContributions are very welcome. Tests can be run with [tox], please ensure
the coverage at least stays the same before you submit a pull request.LicenseDistributed under the terms of theGNU GPL v3.0license,
"napari-tracing" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-trackpy
napari-trackpyPlugin to dotrackpyparticle tracking on 3D microscopy data withinnapari. Currently only tracking of XYZ data is implemented.InstallationYou can installnapari-trackpyviapip:pip install napari-trackpyTo install latest development version :pip install git+https://github.com/rhoitink/napari-trackpy.gitHow to use this plugin?Load your XYZ data (usingnapari-aicsimageio)Make sure to split channels into different layers, such that the layer only contains 3D (XYZ) dataOpen the widget for the tracking plugin viaPlugins>XYZ particle trackingOptimize the tracking settings for your dataset, for an extensive description of the settings, visitthis tutorialSave your tracking data into the.xyzfile format usingCtrl+S(on the points layer) or via the menuFile>Save Selected Layer(s)...ContributingContributions are very welcome. Tests can be run withtox.LicenseDistributed under the terms of theMITlicense,
"napari-trackpy" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-tracks
napari-tracksPlugin for loading tracks layers from csv into napariThisnapariplugin was generated withCookiecutterusing with@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-tracksviapip:pip install napari-tracksContributingContributions are very welcome. Tests can be run withtox, please ensure
the coverage at least stays the same before you submit a pull request.LicenseDistributed under the terms of theBSD-3license,
"napari-tracks" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-tracks-reader
napari-tracks-readerRead tracks from various tracking softwares output files to napari tracks layer.
Supported formats are:Trakmate model (xml)Icy (xml)TrackContestISBI2012 (xml)Thisnapariplugin was generated withCookiecutterusing with@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-tracks-readerviapip:pip install napari-tracks-readerContributingContributions are very welcome. Tests can be run withtox, please ensure
the coverage at least stays the same before you submit a pull request.LicenseDistributed under the terms of theGNU GPL v3.0license,
"napari-tracks-reader" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-trait2d
napari-trait2dA napari plugin for TRAIT2D, a software for quantitative analysis of single particle diffusion dataThisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-trait2dviapip:pip install napari-trait2dTo install latest development version :pip install git+https://github.com/jacopoabramo/napari-trait2d.gitContributingContributions are very welcome. Tests can be run withtox, please ensure
the coverage at least stays the same before you submit a pull request.LicenseDistributed under the terms of theBSD-3license,
"napari-trait2d" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-tyssue
napari-tyssueA napari plugin for use with the tyssue libraryExample video of apoptosis demo simulation created based on the
apoptosis demo fromtyssue-demo.Example video of apoptosis demo simulation created based on work under
revision by Suzanne group at U Toulouse entitled
"Epithelio-mesenchymal transition generates an apico-basal driving
force required for tissue remodeling"available here.Thisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.InstallationYou are better off using conda. You will need pytables, and ideally CGAL.You can installnapari-tyssueviapip:pip install napari-tyssueTo install latest development version :pip install git+https://github.com/kephale/napari-tyssue.gitContributingContributions are very welcome. Tests can be run withtox, please ensure
the coverage at least stays the same before you submit a pull request.LicenseDistributed under the terms of theBSD-3license,
"napari-tyssue" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-ufish
napari-ufishDeep learning-based FISH spot calling method.
The napari plugin forU-FISH.LinksU-FISHU-FISH modelsFISH_spots datasetTODO ListSample imageInference interfaceInference parametersLoad model from pathHelp information dialogTraining interfaceThisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-ufishviapip:pip install napari-ufishContributingContributions are very welcome. Tests can be run withtox, please ensure
the coverage at least stays the same before you submit a pull request.LicenseDistributed under the terms of theMITlicense,
"napari-ufish" is free and open source softwareIssuesIf you encounter any problems, please [file an issue] along with a detailed description.
Package: napari-ui-tracer
napari-ui-tracerA plugin to help understand Napari UI components and locate their code definitionThisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-ui-tracerviapip:pip install napari-ui-tracerOr viaconda:conda install -c conda-forge napari-ui-tracerTo install latest development version :pip install git+https://github.com/dalthviz/napari-ui-tracer.gitUsageShow the plugin inside the napari interface:You can launch napari with the plugin visible running:napari -w napari-ui-tracerOr select it fromPlugins > Napari UI tracer widgetCheck theEnable Qt event filtercheckbox:UseCtrl/Cmd + Mouse button right clickto see the information available about any widget inside napariAn option to show objects documentation (object class docstring) can be used by checking theShow object documentationcheckboxCheck theEnable application events loggingcheckbox:A log like information with the events generated when interacting with the application will appearSome configuration options are available:Stack depth: Stack depth to show. Default to 20Allowed nested events: How many sub-emit nesting levels to show (i.e. events that get triggered by other events). Default to 0If you want to explore the related widget or event module source file, click the link in the output section of the plugin (the module file will open if you have a registered program to open such kind of file)ContributingContributions are very welcome. Pre-commit is used for formatting. Tests can be run withtox, please ensure
the coverage at least stays the same before you submit a pull request.LicenseDistributed under the terms of theMITlicense,
"napari-ui-tracer" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.