Saravanan666/pypi-org huggingface dataset:
Package: napari-ndtiffs
napari-ndtiffsnapari plugin for nd tiff folders with optional CUDA or OpenCL-based deskewing.Built-in support for folders of (skewed) lattice light sheet tiffs.Thisnapariplugin was generated withCookiecutterusing with@napari'scookiecutter-napari-plugintemplate.FeaturesDrag and drop a folder of tiffs onto napari window to view easily(currently designed to detect  lattice light sheet tiffs, but easily
adjustable)If latticeSettings.txtfile is found, will deskew automatically (only if
necessary)Lazily loads dataset on demand.  quickly load preview your data.Handles.ziparchives as well!  Just directly compress your tiff folder,
then drop it into napari.All OpenCL deskewing, works on GPU as well as CPU, falls back to scipy ifPyOpenCLis unavailable.CuPy-based deskewing will work for cards with NVIDIA GPUs that support CUDA.
CuPy 8.x releases should work, although CuPy >= 9 is recommended. IfCuPyis unavailable, thePyOpenCLimplementation is used instead.It would not be hard to support arbitrary filenaming patterns!  If you have a
folder of tiffs with a consistent naming scheme and would like to take advantage
of this plugin, feel free to open an issue!InstallationYou can installnapari-ndtiffsviapip:pipinstallnapari-ndtiffsTo also install PyOpenCL (for faster deskewing):pipinstallnapari-ndtiffs[opencl]On NVIDIA GPUs with CUDA support, theCuPyimplementation may be faster thanPyOpenCL. CuPy also has experimental support for AMD GPUs via HIP/ROCm. See
the CuPyinstallation instructionsUsageIn most cases, just drop your folder onto napari, or useviewer.open("path")Overriding parametersYou can control things like voxel size and deskewing angle as follows:fromnapari_ndtiffsimportparameter_overrideimportnapariviewer=napari.Viewer()withparameter_override(angle=45,name="my image"):viewer.open("path/to/folder",plugin="ndtiffs")Valid keys forparameter_overrideinclude:dx: (float) the pixel size, in micronsdz: (float)the z step size, in micronsdeskew: (bool) whether or not to deskew, (by default, will deskew if angle > 0, or if a lattice metadata file is detected that requires deskewing)angle: (float) the angle of the light sheet relative to the coverslippadval: (float) the value with which to pad the image edges when deskewing (default is 0)contrast_limits: (2-tuple of int) (min, max) contrast_limits to use when viewing the imagename: (str) an optional name for the imageSample dataTry it out with test data:download sample dataYou can unzip if you like, or just drag the zip file onto the napari window.Or, from command line, use:naparipath/to/lls_mitosis.zipDebuggingTo monitor file io and deskew activity, enter the following in the napari console:importlogginglogging.getLogger('napari_ndtiffs').setLevel('DEBUG')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-ndtiffs" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-nibabel
napari-nibabelRead access to some common neuroimaging file formats, thanks to theNiBabelandpydicomlibraries.Also check outnapari-medical-image-formats!Thisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-nibabelviapip:pip install napari-nibabelContributingContributions 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-nibabel" is free and open source softwareIssuesIf you encounter any problems, please [file an issue] along with a detailed description.
Package: napari-nifti
napari-niftiA napari plugin for reading and writing NIFTI files that have the extension .nii or .nii.gz.Thisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-niftiviapip:pip install napari-niftiTo install latest development version :pip install git+https://github.com/MIC-DKFZ/napari-nifti.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 theApache Software License 2.0license,
"napari-nifti" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.Acknowledgementsnapari-nifti is developed and maintained by the Applied Computer Vision Lab (ACVL) ofHelmholtz Imagingand theDivision of Medical Image Computingat theGerman Cancer Research Center (DKFZ).
Package: napari-nikon-nd2
napari-nikon-nd2Opens Nikon ND2 files into napari. This plugin uses thend2readerandpimspython packages.Thisnapariplugin was generated withCookiecutterusing with@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-nikon-nd2viapip:pip install napari-nikon-nd2ContributingContributions 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-nikon-nd2" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.CreditsThisnapariplugin was created usingNapari Delta Vision Readerand
theAllen Institute IOplugin as examples.
Package: napari-nlm
napari-nlmGPU accelerated non local means (NLM) denoising plugin for napari (WIP)currently only supports single-channel 2D or 3D imagesrequires a OpenCL capable GPUInstallationYou can installnapari-nlmvia [pip]:pip install napari-nlmUsageOpen example imageOpen Sample > napari-nlm: noisy bricksAdjust parameterssigma: denoising strength (the larger sigma, the greater the smoothing)patch_radius: size of local patches, 2 or 3 is a good defaultsearch_radius: size of search area around each pixel to find similar patches, 7-11 is a good defaultDenoise by pressingrunLicenseDistributed under the terms of the [BSD-3] license,
"napari-nlm" is free and open source software
Package: napari-nucleaizer
napari_nucleaizerGUI for the nucleaAIzer method in Napari.OverviewThis is a napari plugin to execute the nucleaizer nuclei segmentation algorithm.Main functionalitiesUsing this plugin will be able toLoad your image into Napar, then outline the nuclei.Specify an image folder containing lots of images and an output folder, and automatically segment all of the images in the input folder.If you are not satisfied with the results, you can train your own model:You can use our pretrained models and fine tune them on your data.You can skip the nucleaizer pipeline and train only on your data.Supported image typesWe have several pretrained models for the following image modelities:fluorescent microscopy imagesIHC stained imagesbrightfield microscopy images,among others. For the detailed descriptions of our models, see:https://zenodo.org/record/6800341.How it works?For the description of the algorithm, see our paper: "Hollandi et al.: nucleAIzer: A Parameter-free Deep Learning Framework for Nucleus Segmentation Using Image Style Transfer, Cell Systems, 2020.https://doi.org/10.1016/j.cels.2020.04.003"The original code (https://github.com/spreka/biomagdsb) is partially transformed into a python package (nucleaizer_backend) to actually perform the operations. See the project page of the backend at:https://github.com/etasnadi/nucleaizer_backend.If you wish to use the web interface, check:http://nucleaizer.org.InstallCreate an environment (recommended).Install napari:pip install "napari[pyqt5]". Other methods:https://napari.org/tutorials/fundamentals/installation.htmlInstall the plugin into napari:User mode fromPyPI: start Napari (command line:napari) and select heInstall/Uninstall Plugins...under thePluginsmenu. In the popup, filter fornapari-nucleaizer.Developer mode: clone this project and usepythhon3 -m pip install -e <path>to install the project locallyinto the same evnrionment as napari. It has the advantage that you will have the latest version.RunStart Napari by callingnaparifrom the command line.Then, activate the plugin in thePluginsmenu. If you successfully installed the plugin, you have to see something like this:Further helpSee thedocumentation(work in progress).IssuesUse the github issue tracker if you experinece unexpected behaviour.ContactYou can contact me ine-mailwhere MY-INSTITUTE isbrc.hu.
Package: napari-obj
napari-objA plugin to read .obj filesThisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-objviapip:pip install napari-objTo install latest development version :pip install git+https://github.com/guignardlab/napari-obj.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-obj" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-omaas
napari-omaasnapari-OMAAS stands for Optical Mapping Acquisition and Analysis Software for panoramic heart imagingThis plugin intends to be an analysis and acquisition tool for optical mapping in potentiometric (Vm) or calcium (Ca2+) fluorescence signals obtained from panoramic imaging of intact hearts.This plugin is in a very early developmental/experimental stage so expect very braking changes at anytime. At the momment supports reading images in .sif format from Andor Technologies powered by thesif_parserpython module.UsageThis plugin can read images generated with Andor Technologies cameras. It has been currently tested on Zyla cameras. Just drag and drop an image to the napari GUI, and the image will display. Alternatively, you can programmatically load/read the image within a notebook.import napari

file = "path/to/my/file/my_image.sif"

viewer = napari.Viewer()
viewer.open(path=file, plugin="napari-omaas", name = "my_image")to display the metadata use the standard call to the corresponding layer:viewer.layers['my_image'].metadataIn addition to opening this specific image format (.sif), it allows the users to perform some basic operations and visualization on images, such as normalization, temporal/spatial filters, motion tracking/compenstaion, plot profile, etc.ExamplesThe following example ilustrate how to perform normalization (pixelwise) on a time serie image and plot its 2d profile along the t dimension withing the average data from the ROI selected.The next example shows how to compute action potetnial duration in the same image stack.RoadmapThis plugin is composed of two major components:analysisandacquisition.Bellow is a list of some features this pluggin aims to do.Analysis FeaturesRead sif files from Andor Technologies.Display time profile of ROIs on image sequences.Normalize images.Perform peak analysis of action potential / Calcium traces.Add motion correction.APD analysis.Create activation maps.Segment images and align heart ROIs.Export results and analysis log.Acquisition FeaturesControl Zyla camera for the acquisition of datatest using the PYME moduleReal-time analysis(?)Thisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-omaasviapip:pip install napari-omaasTo install the latest development version (recommended) :pip install git+https://github.com/rjlopez2/napari-omaas.gitContributingContributions are very welcome. Run tests withtox, ensuring
the coverage remains the same before you submit a pull request.LicenseDistributed under the terms of theBSD-3license,
"napari-omaas" is free and open source software.IssuesIf you encounter any problems, pleasefile an issueand a  detailed description.
Package: napari-ome-zarr
napari-ome-zarrA reader for zarr backed OME-NGFF images.Thisnapariplugin was generated withCookiecutterusing with@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-ome-zarrviapip:pip install napari-ome-zarrUsageNapari will useome-zarrto open images that the plugin recognises as ome-zarr.
The image metadata from OMERO will be used to set channel names and rendering settings
in napari::$ napari "https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.3/9836842.zarr/"


# Also works with local files
$ napari 6001240.zarrOR in python::import napari

viewer = napari.Viewer()
viewer.open('https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.3/9836842.zarr/')

napari.run()If single zarray is passed to the plugin, it will be opened without the use of
the metadata::$ napari '/tmp/6001240.zarr/0'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-ome-zarr" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-openfibsem
napari-openfibsemOpenFIBSEM ApplicationsThisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-openfibsemviapip:pip install napari-openfibsemTo install latest development version :pip install git+https://github.com/DeMarcoLab/napari-openfibsem.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-openfibsem" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-organoid-counter
Napari Organoid Counter - Version 0.2 is out!A napari plugin to automatically count lung organoids from microscopy imaging data.Note that this plugin only supports single channel grayscale images.Thisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-organoid-counterviapip:pip install napari-organoid-counterTo install latest development version :pip install git+https://github.com/HelmholtzAI-Consultants-Munich/napari-organoid-counter.gitFor the dev branch you can clone this repo and install with:pip install -e .For installing on a Windows machine via napari, follow the instuctionshere.What's new in v2?Checkout ourWhat's New in v2here.How to use?After installing, you can start napari (either by typingnapariin your terminal or by launching the application) and select the plugin from the drop down menu.For more information on this plugin, its' intended audience, as well as Quickstart guide go to ourQuickstart guide.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-organoid-counter" is free and open source softwareDependenciesnapari-organoid-counteruses thenapari-aicsimageio[1][2]plugin for reading and processing CZI images.[1] Eva Maxfield Brown, Dan Toloudis, Jamie Sherman, Madison Swain-Bowden, Talley Lambert, AICSImageIO Contributors (2021). AICSImageIO: Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in Pure Python [Computer software]. GitHub.https://github.com/AllenCellModeling/aicsimageio[2] Eva Maxfield Brown, Talley Lambert, Peter Sobolewski, Napari-AICSImageIO Contributors (2021). Napari-AICSImageIO: Image Reading in Napari using AICSImageIO [Computer software]. GitHub.https://github.com/AllenCellModeling/napari-aicsimageioIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.CitingIf you use this plugin for your work, please cite it using the following:Christina Bukas, Harshavardhan Subramanian, & Marie Piraud. (2023). HelmholtzAI-Consultants-Munich/napari-organoid-counter: v0.2.0 (v0.2.0). Zenodo.https://doi.org/10.5281/zenodo.7859571bibtex:@software{christina_bukas_2022_6457904,
  author       = {Christina Bukas, Harshavardhan Subramanian, & Marie Piraud},
  title        = {{HelmholtzAI-Consultants-Munich/napari-organoid- 
                   counter: second release of the napari plugin for lung
                   organoid counting}},
  month        = apr,
  year         = 2023,
  publisher    = {Zenodo},
  version      = {v0.2.0},
  doi          = {10.5281/zenodo.7859571},
  url          = {https://doi.org/10.5281/zenodo.7859571}
}
Package: napari-orientationpy
napari-orientationpyAnalyze orientations in 2D, 3D, and RGB images in Napari. This plugin is based on theOrientationpyproject.InstallationYou can installnapari-orientationpyviapip:pip install napari-orientationpyUsageTo get started, open an image in the Napari viewer and startnapari-orientationpyfrom thePluginsmenu:Plugins > Napari Orientationpy > Orientation measurementSelect the structural scale parametersigma. This value control represents the scale at which the image gradients are computed. Try different values ofsigmato understand what works best for your images. A reasonable guess would be the order in size, in pixels, of the structures that you are interested in. For example, if you are imaging fibers that appear to be about 4 pixels wide, try to set a value ofsigma=4.If you are analyzing a 3D image, selectfiberormembranemode. Infibermode, the orientation normals follow fibrous structures. Inmembranemode, the orientations are normal to the surface of membranous structures.Decide which outputs you'd like to visualize.Thecolor-coded orientationis a pixel-wise representation of 3D orientations as colors (similar colors = similar orientations).Theorientation vectorsget rendered in aVectorslayer in Napari. They are sampled on a regular grid defined by theSpacing (X),Spacing (Y)andSpacing (Z)values (for 2D images, theZvalue is ignored). The length of the vectors can be rescaled based on theenergyvalue of the orientation computation.You can also output the localorientation gradient(misorientation).Compute orientation. This button will trigger the orientation computationonly when necessary(i.e. when the value ofsigma, themodeor theimagehave changed). If you only adjust theorientation vectorsparameters, clicking the compute button will update the results very fast.Save orientation (CSV). This will save the orientation measurements as a CSV table with columnsX,Y,Z,theta,phi,energy, andcoherencyfor all the pixels in the image.Plotting the 3D orientation distributionIf you have computedorientation vectorsfor a 3D image, you can plot their spatial distribution as astereographic projectionalong theX,YorZdirection directly in Napari. Select the widget from:Plugins > Napari Orientationpy > Orientation distribution (3D)Sample imagesWe provide a few sample images to test our plugin. Open them from:File > Open Sample > Napari OrientationpyContributingContributions are very welcome. Please get in touch if you'd like to be involved in improving or extending the package.LicenseDistributed under the terms of theBSD-3license,
"napari-orientationpy" is free and open source softwareIssuesIf you encounter any problems, please file an issue along with a detailed description.
Package: napari-owncloud
napari-owncloudUsageBrowse folders and images inowncloud/nextcloudservers and open them using just a double-click!Login to an owncloud or nextcloud server by clicking the menuTools > Utilities > Browse owncloud / nextcloud storageYou can then navigate through folders by double-clickingfolder/items in the list.
You can also open images by double-clicking them. Alternatively, use the arrow-up and arrow-down key to navigate the list and hit ENTER to open an image or folder.Store images in your cloud storage using the buttonSave / upload current layer. Note: Currently, only single selected layers can be saved.DemoInstallationYou can installnapari-owncloudviapip:pip install napari-owncloudRelated pluginsThere are other napari plugins that allow you browsing local and online image storagenapari-omeronapari-folder-browserContributingContributions 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-owncloud" 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-parallel
napari-parallelThis plugin is used for parallel computing of image processing using the code
generation capabilities of thenapari-assistantplugin and the distributed
computing librarydask.Plugin to process images in parallel using several computersThisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-parallelviapip:pip install napari-parallelContributingContributions 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-parallel" is free and open source softwareIssuesIf you encounter any problems, please [file an issue] along with a detailed description.
Package: napari-patchcreator
napari-patchcreatorA simple plugin to create quadratic patches from images through selection and clicking with the left mouse button.
The patches can then be exported to a folder of your own choosing.Thisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-patchcreatorviapip:pip install napari-patchcreatorTo install latest development version :pip install git+https://github.com/juglab/napari-patchcreator.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-patchcreator" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-pdr-reader
napari-pdr-readerA reader plugin for Napari for PDS data powered by the PDR libraryThisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-pdr-readerviapip:pip install napari-pdr-readerTo install latest development version :pip install git+https://github.com/AndrewAnnex/napari-pdr-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-pdr-reader" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.