Saravanan666/pypi-org huggingface dataset:
Package: napari-cursor-tracker
napari-cursor-trackerPlugin for easy manual annotation/tracking of 3D or 2D + t dataset by following the cursor.InstallationYou can installnapari-cursor-trackerviapip:pip install napari-cursor-trackerGetting Started with napari-cursor-trackerWelcome tonapari-cursor-tracker, a tool that simplifies the annotation of points in stacks of images by tracking your cursor's position. This documentation will guide you through the process of setting up and using this plugin effectively.Points Layer SetupBefore you can start tracking, you need to create a points layer, which will store the positions of your cursor for each image in the stack. Here's how to set it up:Choose a Reference Image:Start by selecting a "Reference image" from your image stack. The number of frames or slices in the reference image determines how many points your new layer will have (one per frame/slice).Specify Point Name:Assign a name to the tracked point. This name will also serve as the name for the new layer. This step is particularly useful when tracking multiple points.Create the Layer:Click on "Add new layer" to create the points layer. Initially, all points will be located at the origin (0, 0, 0), but their positions will be updated as you start tracking.Tracking Your CursorNow that you have set up the points layer, you can start tracking your cursor's position. Follow these steps:Select the Active Layer:Choose the points layer where you want to save the tracking results as the "Active layer."Initiate Tracking:Begin tracking your cursor's position by pressing the 't' key on your keyboard. To stop tracking, press 't' again. If the "Auto play when tracking is started" option is enabled, playback will start automatically when you press 't'. Alternatively, you can manually scroll through the images, and your cursor's position will be saved whenever the slice/frame index changes.Customize Playback:To facilitate or expedite tracking, you can adjust playback parameters as needed.Tracking Multiple PointsIf you need to track multiple points of interest, you can follow these steps:Create Individual Layers:Create a separate points layer for each point you want to track.Select Active Layer:Use the "Active layer" dropdown menu to select the specific points layer you want to work with.Start Tracking:Begin tracking the selected point following the previously mentioned tracking process.Saving Your ResultsThe results from your tracking sessions can be saved as CSV files. Any points that were not tracked will be marked at the origin point (0, 0, 0) in the saved file.With these guidelines, you should be well-prepared to efficiently annotate points in your image stacks usingnapari-cursor-tracker. Happy tracking!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 theBSD-3license,
"napari-cursor-tracker" is free and open source softwareIssuesIf you encounter any problems, please [file an issue] along with a detailed description.
Package: napari-curtain
napari-curtainView one image over another as curtainThisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.UsageYou find theCurtainplugin in the menuTools > Visualization > Curtain. Move the position of the slider left/right
as shown in the video above. In case one image is much bright than the other, you can modify thefactorsabove the
slider until visualization pleases.InstallationYou can installnapari-curtainviapip:pip install napari-curtainContributingContributions 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-curtain" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-curviewer
napari-curviewerA plugin to unroll organs along their curved central lineThisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-curviewerviapip:pip install napari-curviewerTo install latest development version :pip install git+https://github.com/Rocsg/napari-curviewer.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 theGNU LGPL v3.0license,
"napari-curviewer" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-czifile2
napari-czifile2Carl Zeiss Image (.czi) file type support for napariOpen .czi files and interactively view scenes co-registered in the machine's coordinate system using napariInstallationYou can install napari-czifile2 viapip:pip install napari-czifile2Alternatively, you can install napari-czifile2 viaconda:conda install -c conda-forge napari-czifile2AuthorsCreated and maintained by Jonas Windhagerjonas.windhager@uzh.chContributingContributingChangelogChangelogLicenseMIT
Package: napari-data-preview
napari-data-previewPreview lightsheet microscopes acquisition, and allow the creation of an XML for importing the data into TeraStitcher.This package is very experimental, and you should expect bug/errors.InstallationYou can installnapari-data-previewvia [pip]:pip install napari-data-previewTo install latest development version :pip install git+https://github.com/WyssCenter/napari-data-preview.git
Package: napari-deepfinder
napari-deepfinderA napari plugin for the DeepFinder library which includes display, annotation, target generation, segmentation and clustering functionalities.
An orthoslice view has been added for an easier visualisation and annotation process.The documentation for users is availablehere.Thisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-deepfinderviapip:pip install napari-deepfinderTo install latest development version :pip install git+https://github.com/deep-finder/napari-deepfinder.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 theGNU GPL v3.0license,
"napari-deepfinder" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-deepmeta
napari-deepmetaMice lungs and metastases segmentation tool.
This tool is a demo tool for DeepMeta network.Thisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-deepmetaviapip:pip install napari-deepmetaTo install latest development version :pip install git+https://github.com/EdgarLefevre/napari-deepmeta.gitUsageThis plugin is designed to process your mouse MRI images with our dataset. It comes with a demo, including one of our
test images.By opening the deepmeta demo plugin, you will see an interface with one unique button, by clicking on it, it will load an image,
run prediction and then draw the masks contours on each slice.If you open the deepmeta plugin, you will see an interface with one button and 3 checkboxes.
By checking the checkboxes, you add steps to the pipeline (enhance contrast, do postprocessing, segment metastases).
Once everything is setup, just click on the button and wait (the waiting time depends on your computer performance.)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-deepmeta" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-DeepSpot
napari-DeepSpotRNA spot enhancement for fluorescent microscopy images.Thisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-DeepSpotviapip:pip install napari-DeepSpotBuild from sourceThis plugin is using Tensorflow, make sure your Python environment has Tensorflow, on create a new environment using the following commands:Conda:conda env create -f environment.ymlconda activate deepspot-napariOr pip:pip install -r requirements.txtUsageOpen one or multiple images using Napari GUI :
File > Open > Select your imageThe images are then displayed on NapariLoad the Plugin:
Plugins > Napari-DeepSpot:Enhance SpotClick on the right panel Button "Enhance"Wait a few seconds for the magic to happen :You can see the original images and the enhanced version in the left panel in the layer section.To save the images : File > Save all layers or File > Save selected layers.CitationIf you use this plugin please cite thepaper:@article {Bouilhol2021DeepSpot,author = {Bouilhol, Emmanuel and Lefevre, Edgar and Dartigues, Benjamin and Brackin, Robyn and Savulescu, Anca Flavia and Nikolski, Macha},title = {DeepSpot: a deep neural network for RNA spot enhancement in smFISH microscopy images},elocation-id = {2021.11.25.469984},year = {2021},doi = {10.1101/2021.11.25.469984},publisher = {Cold Spring Harbor Laboratory},URL = {https://www.biorxiv.org/content/early/2021/11/25/2021.11.25.469984},eprint = {https://www.biorxiv.org/content/early/2021/11/25/2021.11.25.469984.full.pdf},journal = {bioRxiv}}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-DeepSpot" is free and open source softwareKnown IssuesIf you have troubles with the Python packagestyping extensions, use the command :pip install typing-extensions --upgradeWhen using "Enhance" on multiple images, Napari may freeze. Just wait until it comes to life again, the images will still be enhanced. This is due to Napari memory usage and will be fix one day.Other IssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-demo
napari-demoThis is a demo plugin implementation ofhttps://github.com/napari/napari/blob/master/examples/magic_image_arithmetic.pyThisnapariplugin was generated withCookiecutterusing with@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-demoviapip:pip install napari-demoContributingContributions 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-demo" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
To report security issues, seesecurityCode of ConductThis project adheres to the Contributor Covenantcode of conduct. By participating, you are expected to uphold this code. Please report unacceptable behavior toopensource@chanzuckerberg.com.
Package: napari-denoiseg
napari-denoisegA napari plugin performing joint denoising and segmentation of microscopy images usingDenoiSeg.----------------------------------InstallationCheck out thedocumentationfor more detailed installation
instructions.Quick demoYou can try out a demo by loading theDenoiSeg Demo predictionplugin and directly clicking onPredict.DocumentationDocumentation is available on theproject website.Contributing and feedbackContributions are very welcome. Tests can be run withtox, please ensure
the coverage at least stays the same before you submit a pull request. You can also
help us improve byfiling an issuealong with a detailed description or contact us
through theimage.scforum (tag @jdeschamps).Cite usTim-Oliver Buchholz, Mangal Prakash, Alexander Krull and Florian Jug, "DenoiSeg: Joint Denoising and Segmentation"arxiv(2020)AcknowledgementsThis plugin was developed thanks to the support of the Silicon Valley Community Foundation (SCVF) and the
Chan-Zuckerberg Initiative (CZI) with the napari Plugin Accelerator grant2021-239867.Distributed under the terms of theBSD-3license,
"napari-denoiseg" is a free and open source software.
Package: napari-dexp
napari-DEXPA plugin to interfaceDEXPwithnapari.Thisnapariplugin was generated withCookiecutterusing with@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-dexpviapip:pip install napari-dexpContributingContributions 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-dexp" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-dv
napari-dvDeltavision/MRC file reader for napari.This wraps themrclibrary.See alsonapari-aicsimageio, which also uses themrcto provide dv file support,
along with many other common file formats.InstallationYou can installnapari-dvviapip:pip install napari-dvContributingContributions 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-dv" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-dvid
napari-dvidDVID loader for napari, from a urlThisnapariplugin was generated withCookiecutterusing with@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-dvidviapip:pip install napari-dvidExamplesOnce installed, runnapari --with napari-dvidto get the plugin sidebar:Paste in a URL to a DVID volume and hit "Load" to load the volume! As an example, try:https://emdata.janelia.org/api/node/ab6e610d4/grayscale/raw/0_1_2/256_256_256/7500_7000_4400ContributingContributions 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-dvid" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-dzi-zarr
napari-dzi-zarrAn experimental plugin for viewing Deep Zoom Images (DZI) with napari + zarr + dask.Thisnapariplugin was generated withCookiecutterusing with@napari'scookiecutter-napari-plugintemplate.DescriptionTheDZI File Formatis a pyramidal tile source specification where individual tiles are RGB/RGBA JPEG/PNG images.
DZI is a very popular tile source for zoomable web-viewers likeOpenSeadragon, and as a result many tile sources are available over
HTTP. This plugin wraps a DZI tile source (local or remote) as a multiscale Zarr, where each pyramidal level is azarr.Arrayof shape(level_height, level_width, 3/4), allowing the same images to be viewed
innapari+dask.InstallationYou can installnapari-dzi-zarrviapip:pip install napari-dzi-zarrUsageThis high-resolution scan of Rembrandt's Night Watch is available thanks toR.G Erdmann. More examples can be found onboschproject.org.$ napari http://hyper-resolution.org/dzi/Rijksmuseum/SK-C-5/SK-C-5_VIS_20-um_2019-12-21.dziContributingContributions are very welcome. Tests can be run withtox.LicenseDistributed under the terms of theBSD-3license,
"napari-dzi-zarr" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-ehooke
napari-ehookeeHooke implementation within napariThisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-ehookeviapip:pip install napari-ehookeTo install latest development version :pip install git+https://github.com/antmsbrito/napari-ehooke.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-ehooke" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-elementary-numpy-operations
napari-elementary-numpy-operationsA napari plugin covers elementary numpy operations like swap axes, flip, sqeeze an array or rotate an arrays by 90° steps.InstallationYou can installnapari-elementary-numpy-operationsviapip:napari-elementary-numpy-operationsContributingContributions 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-elementary-numpy-operations" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-EMD
napari-EMDA simple plugin to view .emd files in napari (i.e. Velox files). Allows users to track metadata as it changes over the course of a video/stack, developed for analysis of in-situ microscopy data, where users may be changing magnification, focus, etc. during aquisition.Thisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-EMDviapip:`pip install napari-EMD`You can install napari and access the plugin through the GUI.Reccomended install command for napari:`python -m pip install "napari[all]"`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 theBSD-3license,
"napari-EMD" is free and open source softwareIssues and RequestsWarning: The metadata viewer does not work in the currentNapari bundleversion (August 2023). Use thepython package versionof Napari for this feature.If you encounter any problems or would like any functionality added, pleasefile an issuealong with a detailed description.Current maintainer(s):Nicki ShawPreviewImages A and B show different frames in the same image stack, the metadata plugin on the right shows the changing focus value.To DoAttatch last-opened information, so the widget does not reset when frames are changed and open toggle options are open remain.Add a search bar for navigating metadata.Output metadata as file option.Add note to change order of open files to replacee active metadata view.Make Singleframe note update automatically on change of file order.
Package: napari-em-reader
napari-em-readerA napari plugin to read .em filesThisnapariplugin was generated withCookiecutterusing with@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-em-readerviapip:pip install napari-em-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 theBSD-3license,
"napari-em-reader" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-explorer
napari-explorerBrowse files in a folder, filter, and open within napariThisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-explorerviapip:pip install napari-explorerContributingContributions 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-explorer" is free and open source softwareIssuesIf you encounter any problems, please [file an issue] along with a detailed description.
Package: napari-features-selector
napari-features-selectorAn interactive plugin that enables users to choose the important/relevant features from a set of multiple features. These selected features can then be applied to various tasks like object detection, segmentation, classification, among others.Thisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-features-selectorviapip:pip install napari-features-selectorContributingContributions 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-features-selector" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-figure
napari-figureMaking Figure with napari more easilyThisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-figureviapip:pip install napari-figureTo install latest development version :pip install git+https://github.com/romainGuiet/napari-figure.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-figure" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-filament-annotator
3D Filament Annotator3D Filament Annotator is a tool for annotating filaments and other curvilinear structures in 3D.
The 3D annotation is done by annotating the filament in two different projections,
calculating intersection, and refining the filament position with active contours.InstallationInstall naparipip install napari[all]Install the filament annotatorpip install git+https://github.com/amedyukhina/napari-filament-annotator.gitUsageFor detailed usage instructions, please refer to theusage tutorial.ContributingContributions are very welcome both with regard to plugin functionality, and
tips on using it and setting parameters.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 theApache Software License 2.0license,
"napari-filament-annotator" is free and open source softwareDependenciesnapariscikit-imagescikit-learnNetworkXGeometry3DIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.Thisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.
Package: napari-filaments
napari-filamentsA napari plugin for filament analysis.This plugin helps you to manually track filaments using path shapes ofShapeslayer.Currently implemented functionsFit paths to filaments in an image as a 2-D spline curve.Clip/extend paths.Measurement of filament length at sub-pixel precision.Basic quantification (mean, std, etc.) along paths.Import paths from ImageJ ROI file.Basic UsageClickLayers > open imageto open a tif file. You'll find the image you chose and a shapes layer are added to the layer list.The "target filaments" box shows the working shapes layer.The "target image" box shows the image layer on which fitting and quantification will be conducted.The "filament" box shows currently selected shape (initially this box is empty).Add path shapes and push keyF1to fit the shape to the filament in the target image layer.In the "Spline" tab, you can cut/extend or re-fit splines.In the "Measure" tab, click "measure property" to measure mean instensity etc along each spline.How it worksSpline fitting is done as following.Thisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-filamentsviapip:pip install napari-filamentsTo install latest development version :pip install git+https://github.com/hanjinliu/napari-filaments.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-filaments" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.