Saravanan666/pypi-org huggingface dataset:
Package: napari-mclabel
Napari McLabelWhat is the purpose of this tool?McLabel is a semi-automatic local thresholding tool that can help to label cellular objects such as macrophages in fluorescence microscopy images. In cases where a global threshold does not yield satisfactory results, a local threshold based on a ROI drawn by the user may give better results. See the video for an example:InstallationThe plugin can be installed using pip:pipinstallnapari-mclabelAfter succesfull installation the plugin will appear in the plugins menu of napari.UsageThe GUI of McLabel lives in the right pane of napari. If multiple layers are loaded, select the layer that you want to segment. The theshold finding algorithm is by default is triangle, however there are plenty of alternatives and depending on the data another algorithm might be better suited.Press "Draw Label"Draw a rough outline around the object of interest.Press "Compute Label"If not satisfied with result, adjust threshold using the sliderContinue with next objectReferenceIf you use McLabel in your work, consider citing our background paper:https://doi.org/10.1007/978-3-658-41657-7_20@InProceedings{10.1007/978-3-658-41657-7_20,
author="Utz, Jonas
and Schlereth, Maja
and Qiu, Jingna
and Thies, Mareike
and Wagner, Fabian
and Brahim, Oumaima B.
and Gu, Mingxuan
and Uderhardt, Stefan
and Breininger, Katharina",
editor="Deserno, Thomas M.
and Handels, Heinz
and Maier, Andreas
and Maier-Hein, Klaus
and Palm, Christoph
and Tolxdorff, Thomas",
title="McLabel",
booktitle="Bildverarbeitung f{\"u}r die Medizin 2023",
year="2023",
publisher="Springer Fachmedien Wiesbaden",
address="Wiesbaden",
pages="82--87",
abstract="In this work, we present a semi-automatic labelling tool for the annotation of complex cellular structures such as macrophages in fluorescence microscopy images. We present McLabel, a napari plugin that allows users to label structures of interest by simply scribbling outlines around the area of interest, using the triangle thresholding method with post-processing to identify the desired structure. Additionally, manual adaption of the threshold allows for quick and fine-grained local correction of the segmentation. The tool is evaluated in a user study with five experts, who annotated images both with and without the tool. The results show that variability in annotations between experts is reduced when the labelling tool is used and annotation time is reduced by a factor of five on average.",
isbn="978-3-658-41657-7"}
Package: napari-medical-image-formats
napari-medical-image-formatsA Plugin in order to read and write medical image formats such as DICOM, DICOM Series and NIfTI. The meta information is supported by the package napari-itk-io.InstallationYou can installnapari-medical-image-formatsviapip:pip install napari-medical-image-formatsContributingContributions 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-medical-image-formats" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-meshio
napari-meshioThis napari plugin usesmeshioto read and write mesh files to surfaces in napari.Image caption: screenshot of theStanford bunnyexample surface mesh open in napari.InstallationHow to use napari-meshioRead surface data from fileOpen example surface dataSave surface dataSupported mesh file formatsContributingLicenseIssuesInstallationYou can installnapari-meshioviapip:pip install napari-meshioTo install latest development version :pip install git+https://github.com/GenevieveBuckley/napari-meshio.gitHow to use napari-meshioRead surface data from fileDrag and drop the file onto the napari viewer.Note:Hereare a number of.plyexample files you can download to try, likethis airplane(seeimage).Open example surface dataLaunch the napari viewer, then open one of the sample datasets (eg: theStanford bunny) from the file menu:File>Open Sample>napari-meshio>bunnyOr, open sample data from python with:importnapariviewer=napari.Viewer(ndisplay=3)viewer.open_sample('napari-meshio','bunny')Save surface dataTo save a surface layer, click the layer name to select it, and then choose save from the file menu:File>Save selected layer(s)You can also use keyboard shortcuts to save the selected surface layer:Windows/Linux:Control+SMac:⌘+SOr, save surface layers from python with:filename="bunny.stl"viewer.layers['bunny'].save(filename)Note: this code example assumes you have the Stanford bunny example dataset loaded.Awide variety of surface mesh file formats are supportedbymeshio.
If no file extension is provided when saving a surface layer,
the default is the.plypolygon file format.Supported mesh file formatsNote: Only triangular mesh faces are supported by napari.Themeshiolibrary documentation describes the supported file formats:There are various mesh formats available for representing unstructured meshes.
meshio can read and write all of the following and smoothly converts between them:Abaqus(.inp),
ANSYS msh (.msh),AVS-UCD(.avs),CGNS(.cgns),DOLFIN XML(.xml),Exodus(.e,.exo),FLAC3D(.f3grid),H5M(.h5m),Kratos/MDPA(.mdpa),Medit(.mesh,.meshb),MED/Salome(.med),Nastran(bulk data,.bdf,.fem,.nas),Netgen(.vol,.vol.gz),Neuroglancer precomputed format,Gmsh(format versions 2.2, 4.0, and 4.1,.msh),OBJ(.obj),OFF(.off),PERMAS(.post,.post.gz,.dato,.dato.gz),PLY(.ply),STL(.stl),Tecplot .dat,TetGen .node/.ele,SVG(2D output only) (.svg),SU2(.su2),UGRID(.ugrid),VTK(.vtk),VTU(.vtu),WKT(TIN) (.wkt),XDMF(.xdmf,.xmf).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-meshio" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.Thisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.
Package: napari-micromanager
napari-micromanagerGUI interface between napari and micromanager powered bypymmcore-plusandpymmcore-widgets🚧 Experimental!  Work in progress!  Here be 🐲 🚧InstallationYou can installnapari-micromanagerviapip:pip install napari-micromanagerGetting micromanager adapters:The easiest way to get the micromanager adapters is to use:mmcore installthis will install micromanager to the pymmcore_plus folder in your site-package; use this to see where:python -c "from pymmcore_plus import find_micromanager; print(find_micromanager())"alternatively, you can direct pymmcore_plus to your own micromanager installation with theMICROMANAGER_PATHenvironment variable:export MICROMANAGER_PATH='/path/to/Micro-Manager-...'ContributingContributions are very welcome.Launching napari with pluginYou can launch napari and automatically load this plugin using thelaunch-dev.pyscript:pythonlaunch-dev.pyAlternatively you can run:napari-wnapari-micromanagerLicenseDistributed under the terms of theBSD-3license,
"napari-micromanager" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-microscope
Microscope control plugin for Napari via Python Microscope.Current development stage is whatever comes before alpha and “proof of
concept”.To testI haven’t had access to real hardware yet, so this has all been
developed with simulated devices.Start the device server with simulated devices.Create a device server configuration file like so:import microscope
from microscope.device_server import device
from microscope.simulators import (
    SimulatedCamera,
    SimulatedFilterWheel,
    SimulatedLightSource,
    SimulatedStage,
)

DEVICES = [
    device(SimulatedCamera, "localhost", 8000,),
    device(SimulatedLightSource, "localhost", 8001),
    device(SimulatedFilterWheel, "localhost", 8002,
           {"positions": 6}),
    device(SimulatedStage, "localhost", 8003,
           {"limits": {"X": microscope.AxisLimits(0, 25000),
                       "Y": microscope.AxisLimits(0, 12000)}}),
]Start the device server (ensure port 8000-8003 are unused):$ device-server path-to-microscope-config.pyStart napariPlugins > Add Dock Widget > microscope: MicroscopeWidgetConnect to the camera:On the new widget, click on the “Add device” button.Enter the camera URIPYRO:SimulatedCamera@localhost:80005. Tick theEnabledbox to enable the camera and then press the
“Snap” button.6. A random values image will appear displayed on the napari viewer.
Keep pressing the “Snap” button to get new images.  The top left
corner of the image is the simulated image number.Connect to the other simulated devices.  Their URIs are:PYRO:SimulatedLightSource@localhost:8001PYRO:SimulatedFilterWheel@localhost:8002PYRO:SimulatedStage@localhost:80038. Changing the other simulated devices, doesn’t really do much (but
does change state of the devices, as can be seen in the logs)Test with stage aware cameraThis is pretty much the same as before but one can use a large RGB
TIFF (histology samples are perfect) to simulate a camera that returns
subsections of the image file based on the simulated stage position.For quick example, try:wget https://zenodo.org/record/1445489/files/B0002.tifAnd use the following device server configuration file:from microscope.device_server import device
from microscope.simulators.stage_aware_camera import simulated_setup_from_image

DEVICES = [
    device(simulated_setup_from_image, "localhost", 8000,
           conf={"filepath": "B0002.tif"}),
]The URI for the devices will be:PYRO:camera@localhost:8000
PYRO:filterwheel@localhost:8000
PYRO:stage@localhost:8000Changing the filterwheel changes which channel from the image is
returned.  Changing the stage coordinates changes the image that is
returned (but beware of the corners, pixels outside the image size are
not handled yet and will give an error).
Package: napari-microtubule-analyzer
napari-microtubule-analyzerA plugin to analyze microtubule organizationThisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-microtubule-analyzerviapip:pip install napari-microtubule-analyzerTo install latest development version :pip install git+https://github.com/krentzd/napari-microtubule-analyzer.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 theMITlicense,
"napari-microtubule-analyzer" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-molecule-reader
napari-molecule-readerA napari plugin that read molecular structure files. It reads PDB and MMCIF files usingatomium, expanding molecular assemblies to a full visualization. Data is loaded into napari asPointsfor ball representation andVectorsfor stick representation. If multiple models or assemblies are detected, they will be loaded as separate objects.https://user-images.githubusercontent.com/23482191/150109390-bd7fb3b4-79b4-43da-aafc-20921714df25.mp4TODO list:[] handle alternate locations (i.e: different conformations in the same pdb model)Thisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-molecule-readerviapip:pip install napari-molecule-readerTo install latest development version :pip install git+https://github.com/brisvag/napari-molecule-reader.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-molecule-reader" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-morphodynamics
napari-morphodynamicsThis plugin offers an interface for theMorphodynamicspackage which allows to study the shape and intra-cellular dynamics of cells imaged as time-lapses by fluorescence microscopy. The plugin offers a single place to perfrom segmentation, windowing (partition cells into small regions of interests that are tracked over time) and results visualization. The software depends onnapari-convpainta pixel-classifier and/or oncellposefor segmentation.InstallationYou can install the plugin viapipwith:pip install napari-morphodynamicsTo install latest development version :pip install git+https://github.com/guiwitz/napari-morphodynamics.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-morphodynamics" is free and open source softwareAuthorsThis plugin has been developed by Guillaume Witz and Ana Stojiljkovic at the Data Science Lab, University of Bern, in collaboration with Lucien Hinderling and Olivier Pertz from the Pertz Lab, University of Bern. Development has been partially funded by aChan Zuckerberg Initiative grant.IssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-mouse-controls
napari-mouse-controlsControl zoom, slicing and contrast windowing with mouse and touch screenUsageYou find the mouse control panel in the menuTools > Utilities > Mouse controlsZoomAfter clicking the Zoom button, you can click in the napari canvas and move the mouse up and down to zoom in and out.SlicingAfter clicking the Slicing button, you can control the currently displayed slice by moving the mouse.
By moving the mouse up and down, you control the currently selected Z-plane.
By moving the mouse left and right, you control the currently seleted time point.WindowingAfter clicking the Windowing button, you can modify the brightness and contrast by moving the mouse.
By moving the mouse up and down, you control window width of the range of displayed grey values (max - min).
By moving the mouse left and right, you control the center of the grey value window.Normal / default modeClick the Default buttonto return to napari's normal mode.Thisnapariplugin was generated withCookiecutterusing with@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-mouse-controlsviapip:pip install napari-mouse-controlsContributingContributions 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-mouse-controls" is free and open source softwareIssuesIf you encounter any problems, please create a thread onimage.scalong with a detailed description and tag@haesleinhuepf.
Package: napari-mrcfile-handler
napari-mrcfile_handlerA simple plugin to read, write and adjust mrcfiles in napari.Thisnapariplugin was generated withCookiecutterusing with@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-mrcfile_handlerviapip:pip install napari-mrcfile_handlerContributingContributions 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-mrcfile_handler" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-mrcfile-reader
napari-mrcfile-readerRead MRC format image files into napari using themrcfilepackage fromCCP-EMThisnapariplugin was generated withCookiecutterusing with@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-mrcfile-readerviapip:pip install napari-mrcfile-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-mrcfile-reader" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-mri
napari-mriA simple plugin to use with napari for 3D-viewing of Magnetic Resonance Imaging file formatsThisnapariplugin was generated withCookiecutterusing with@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-mriviapip:pip install napari-mriContributingContributions 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-mri" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-mzarr
napari-mzarrA reader and writer plugin for the Mzarr image format.Thisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-mzarrviapip:pip install napari-mzarrContributingContributions 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 theApache Software License 2.0license,
"napari-mzarr" is free and open source softwareIssuesIf you encounter any problems, please [file an issue] along with a detailed description.
Package: napari-n2v
napari-n2vA self-supervised denoising algorithm now usable by all in napari.----------------------------------InstallationCheck out thedocumentationfor more detailed installation
instructions.You can then start the napari plugin by clicking on "Plugins > napari_n2v > Training",
or run the plugin directly from ascript.Quick demoYou can try out a demo by loading theN2V Demo predictionplugin and directly clicking onPredict. This model was trained using theN2V2 example.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).CitationsN2VAlexander Krull, Tim-Oliver Buchholz, and Florian Jug. "Noise2void-learning denoising from single noisy images."Proceedings of the IEEE/CVF conference on computer vision and pattern recognition. 2019.structN2VColeman Broaddus, et al. "Removing structured noise with self-supervised blind-spot networks."2020 IEEE 17th
International Symposium on Biomedical Imaging (ISBI). IEEE, 2020.N2V2Eva Hoeck, Tim-Oliver Buchholz, et al. "N2V2 - Fixing Noise2Void Checkerboard Artifacts with Modified Sampling Strategies and a Tweaked Network Architecture", arXiv (2022).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 grant2021-240383.Distributed under the terms of theBSD-3license,
"napari-n2v" is a free and open source software.
Package: napari-nanopyx
napari-nanopyxnapari plugin ofNanoPyx(the successor to NanoJ) - focused on light microscopy and super-resolution imaging.Thisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-nanopyxviapip:pip install napari-nanopyxUser DocumentationYou can find installation and usage instructions in thewiki.ContributingContributions are very welcome.
Please read ourContribution Guidelinesto know how to proceed.LicenseDistributed under the terms of theCC-By v4.0license,
"napari-nanopyx" is free and open source softwareIssuesIf you encounter any problems, please [file an issue] along with a detailed description.CitingIf you found this work useful, please cite:preprintand
Package: napari-napari
napari-napariA viewer of the napari viewer.https://user-images.githubusercontent.com/21022743/233817006-67ab4165-0b9a-46aa-9731-5964448252de.mp4Thisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-napariviapip:pip install napari-napariTo install latest development version :pip install git+https://github.com/jookuma/napari-napari.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-napari" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-nasa-samples
napari-nasa-samplesThis napari plugin writtenby Loic A. Royerprovides sample datasets from NASA.
In particular, you can access directly from napari the recently released images for theJames Webb Space Telescope, as well as
some of the classic and most beautiful images obtained by the venerable and still strongHubble Space Telescope.
More images will be added over time.Thanks to (NASA)[https://www.nasa.gov/] for releasing these incredible images!Thisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-nasa-samplesviapip:pip install napari-nasa-samplesTo install latest development version :pip install git+https://github.com/royerloic/napari-nasa-samples.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 theMozilla Public License 2.0license,
"napari-nasa-samples" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-nd2-folder-viewer
napari-nd2-folder-viewerLook through separate nd2 files in one viewer.Thisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-nd2-folder-viewerviapip:pip install napari-nd2-folder-viewerTo install latest development version :pip install git+https://github.com/gatoniel/napari-nd2-folder-viewer.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-nd2-folder-viewer" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-nd-cropper
napari-nd-cropperA napari plugin in order to crop nd-images via different modes:Cropping via Drag&Drop interaction box (available for napari releases > 0.4.12)Cropping of double-clicked regions based on predefined size (Integer or Tuple of integer)Cropping based on viewCropping via SlidersInstallationYou can installnapari-nd-cropperviapip:pip install napari-nd-cropperContributingContributions 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-nd-cropper" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.