Saravanan666/pypi-org huggingface dataset:
Package: napari-file-watcher
File watcher plugin for napari (napari-file-watcher)This plugin contains two widgets: file watcher and script editor.Usage: file watcherThe file watcher monitors a folder and displays its images (tiff, ome-zarr or hdf5) as napari layers, watch the following video for a demo:Instructions:Select the folder you want to monitor by pressing "Browse".Select the extension of the files: "zarr", "hdf5" or "tiff".Click "Watch and run" to display the current items & the newly arrived as napari layers.If you click in one of the files of the list, the metadata will show (for hdf5 and zarr)Usage: scripting editorThe script editor is for developing scripts and saving them in the filesystem.
We have used this widget in the context of developing scripts for microscopy control software that implements another file watcher.Instructions:Select the folder where you want to save your scripts in "Browse".Type the name of the script in the edit box below.Click "Add" for saving it into the folder after typing, or "Open" to display an existing file.InstallationYou can installnapari-file-watchervia [pip]:pip install napari-file-watcherOr if you plan to develop it:git clone https://github.com/kasasxav/napari-file-watcher
cd napari-file-watcher
pip install -e .If there is an error message suggesting that git is not installed, runconda install git.ContributingContributions are welcome, tests are run with pytest.IssuesIssues can be reported at:https://github.com/kasasxav/napari-file-watcher/issues
Package: napari-floodfill
🌊 napari-floodfillInteractive object annotation in Napari using aflood filltool. This tool is based on thefloodfunction of Scikit-image.InstallationYou can installnapari-floodfillviapip:pip install napari-floodfillUsageSelect the plugin from thePluginsmenu of Napari.Open an image to annotate (2D, RGB, 2D+t, or 3D).Click on the button "Start flood fill" or pressS. A newLabelslayerFlood fill (current edit)should appear.With theFlood filllayer selected, move your cursor arounda nd click on the image to annotate objects.Double-click to confirm the annotation of an object and move to the next.Options and parametersAuto-increment label index: Tick this option to increment the label index every time a new object is annotated (e.g. if you are annotating multiple objects).Intensity range: Pixels outside of this range will not trigger the flood fill computation. The extremities of the range represent the absolute minimum and maximum of the image. Set the range somewhere to the left if you are annotating dark objects on a bright background, or to the right if you are annotating bright objects.Flood fill tolerance: Controls the extent of the flood fill. A higher value will fill more pixels. The value selected is relative to the image intensity range.ContributingContributions 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-floodfill" is free and open source softwareIssuesIf you encounter any problems, please file an issue along with a detailed description.Thisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.
Package: napari-folder-browser
napari-folder-browserBrowse folders of images and open them using double-click or . You can also navigate through the list using arrow up/down keys.Thisnapariplugin was generated withCookiecutterusing with@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-folder-browserfrom within napari by clicking menuPlugins > Install/uninstall Plugins...and entering here:You can installnapari-folder-browserviapip:pip install napari-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-folder-browser" 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-geojson
napari-geojsonRead and write geojson files in napari.Thisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-geojsonviapip:pip install napari-geojsonTo install latest development version :pip install git+https://github.com/tdmorello/napari-geojson.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-geojson" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-geoscience-viewer
napari-geoscience-viewerA napari plugin for visualizing geoscience HDF5 and netCDF dataNotes on this current version:Xarray is used to visualize netCDF, and h5py is used for HDF5. The dimensions stored in HDF5 doesn't work easily with xarray, so h5py is used instead.For netCDF, it displays world map as a napari shape layer. This only works well for entire globe domain, not for a regional domain, which will be added in future.Map projections are not available yet.
Package: napari-griottes
napari-griottesUse🍒Griottes🍒in napari!https://user-images.githubusercontent.com/11408456/224119160-c381091d-8275-449e-9cf4-679ab474acd2.mp4InstallationInstall from napariYou can installnapari-griottesviapip:pip install napari-griottesTo install latest development version :pip install git+https://github.com/BaroudLab/napari-griottes.gitUsageStarting with labels:Open the plugin in Plugins/napari-griottesMake sure the layer with labels is selectedClick Run once to get centersClick Run second time to get graphSelect the right kind of graph in the drop-down menuAdjust the distanceAdjust thicknesshttps://user-images.githubusercontent.com/11408456/167825581-47c39884-34cf-4b5c-ad84-a4572217559d.mp4Starting with Segmented cellsOpen sample data: File / Open Sample / napari-griottes / Zebrafish 2D with labelsSelect the top layer and covert it to labels (right click - Convert to labels)Run the plugin once to get the centers of labelsRun the plugin twice to get the connectionsProceed with graph creationhttps://user-images.githubusercontent.com/11408456/168237170-b43afd5a-26a4-4cdc-bc42-d3f46f138536.mp4Saving and recovering the graphAny graph you see in napari can be saved in .json format.Select he layers with connectionsClick File/Save Selected LayerChoose Griottes in drop-down menuSaveIn order to recover a previously saved graph in napari, you can simply drag-n-drop your file into napari, or use file open fialog.https://user-images.githubusercontent.com/11408456/167845853-e7071199-3f58-4d11-8d7b-c1358a150e6b.mp4ContributingContributions 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-griottes" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-gruvbox
napari-gruvboxGruvbox theme for napari. Colors are taken from the palette inhttps://github.com/morhetz/gruvbox.Thisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-gruvboxviapip:pip install napari-gruvboxTo install latest development version :pip install git+https://github.com/brisvag/napari-gruvbox.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-gruvbox" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-h5
napari-h5A file reader plugin for napariIt opens simple *.h5 files. Reads all Datasets inside the file and converts to
a napari Image object (np.array).It can also save "image" or "labels" data. Note that these will be saved individually.It does not support data organised internally in "groups".
For these more complicated h5 data structures please try other plugins.Thisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-h5viapip:pip install napari-h5ContributingContributions 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-h5" is free and open source softwareIssuesIf you encounter any problems, please [file an issue] along with a detailed description.
Package: napari-hdf5-labels-io
napari-hdf5-labels-ionapari plugin to store napari projects in a .h5 file. Label layer are stored in a sparse representation (COO list).Thisnapariplugin was generated withCookiecutterusing with@napari'scookiecutter-napari-plugintemplate.DescriptionThis napari plugin provides a writer and reader to store existing layers in the current napari window, all the metadata is stored as well in a HDF5 file. All the stored preferences are included when a project file is opened.Label layers are stored in a coordinate list sparse representation with theSparse moduleto keep the project file size minimum when possible (aiming to implement this in other layers in the future).HDF5 file architectureThe project file is a HDF5 generated with theh5py module. The file groups correspond to the different napari layer types and the layer metadata is stored as attributes of each layer.In the case of the meta dictionary which is nested in the LayerData meta dictionary (napari IO), new keys are generated in the outer dictionary to use them as h5 dataset attributes. This nested dictionary architecture is reconstructed by the reader to ensure format compatibility.InstallationYou can installnapari-hdf5-labels-ioviapip:pip install napari-hdf5-labels-ioContributingContributions 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-hdf5-labels-io" is free and open source software.IssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-help
napari-helpHelpful tooltips for napari.Thisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-helpviapip:pip install napari-helpTo install latest development version :pip install git+https://github.com/brisvag/napari-help.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-help" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-hierarchical
napari-hierarchicalHierarchical file format support for napariThisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-hierarchicalviapip:pip install "napari-hierarchical[all]"To install latest development version :pip install "git+https://github.com/BodenmillerGroup/napari-hierarchical.git#egg=napari-hierarchical[all]"UsageThe plugin enables the reading, editing and writing of container formats. In the plugin,groupsrepresent hierarchically structured collections ofarrays. Each group can hold zero or more arrays and can have zero or more child groups (hierarchical structure). An array is a logical representation of (image) data on disk and directly corresponds to a napari layer when loaded.Files can be opened through napari (e.g.File -> Open File(s)menu,Viewer.open(...)function), as the plugin implements napari's file reader hook. Upon opening a hierarchically structured file, theGroupsandArrayswidgets are displayed. TheGroupswidget allows to browse and restructure the groups tree, while theArrayswidget groups arrays from the selected groups by file format-specific metadata (e.g. channel name for MCD files). Selecting arrays also selects the corresponding napari layers, allowing to adjust their properties.Arrays can be loaded individually by toggling theirloadedstate (circular button), which will add napari layers for the corresponding arrays. Similarly, loaded arrays can be shown or hidden by toggling theirvisiblestate (eye button), which will toggle the visibility of the associated napari layers. The loaded/visible states of groups (collections of arrays) can be toggled in a similar fashion. Arrays are always loaded into memory (no memory mapping), to allow for editing the tree structure. Loaded root groups can be exported to supported hierarchical file formats.Currently, reading/writing of HDF5 and Zarr (not: OME-NGFF) files are supported out of the box, as well as reading imaging mass cytometry (IMC) data (i.e., MCD files). For these file formats, sample data is available through the plugin. Additional readers/writers can be implemented using a pluggy-based interface, similar to the first generationnapari-plugin-engine.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-hierarchical" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-hippo
napari-hippoA large and slightly clumsy plugin for viewing and analysing hyperspectral data in Napari.InstallationYou can installnapari-hippovia [pip]:pip install napari-hippoContributingContributions are very welcome :blush:LicenseDistributed under the terms of the [MIT] license,
"napari-hippo" is free and open source softwareIssuesIf you encounter any problems, please [file an issue] along with a detailed description.CitationA citation for this plugin will be announced shortly.
Package: napari-IDS
napari-IDSA simple plugin to use with napariThisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-IDSviapip:pip install napari-IDSTo install latest development version :pip install git+https://github.com/githubuser/napari-IDS.gitFirst utilisationSuggested environment :Python 3.8IDS 1.2.0.5 version installedTo use this package for the first time :Install Naparipip install "napari[all]"Install napari-IDS packageInstall IDS Python api thanks to the commandids_packagesIf your environment is not the suggested environment, you have to install IDS packages manually.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-IDS" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-imagej
napari-imagejAnapariplugin for access toImageJ2napari-imagejaims to provide access to allImageJ2functionality through thenaparigraphical user interface. It builds on the foundation ofPyImageJ, a project allowing ImageJ2 access from Python.With napari-imagej, you can access:The napari-imagej widget, providingheadless accessto:ImageJ2 Commands- 100+ image processing algorithmsImageJ Ops- 500+functionalimage processing algorithmsSciJava Scripts- migrated from Fiji or ImageJ2, or written yourself!The ImageJ user interface, providing access tothe entire ImageJ ecosystemwithin napari.See theproject roadmapfor future directions.Getting StartedLearn more about the projecthere, or jump straight toinstallation!UsageImage Processing with ImageJ OpsPuncta Segmentation with SciJava ScriptsTroubleshootingTheFAQoutlines solutions to many common issues.For more obscure issues, feel free to reach out onforum.image.sc.If you've found a bug, pleasefile an issue!ContributingWe welcome any and all contributions made onto the napari-imagej repository.Development discussion occurs on theImage.sc Zulip chat.For technical details involved with contributing, please seehereLicenseDistributed under the terms of theBSD-2license,
"napari-imagej" is free and open source software.
Package: napari-image-stacker
napari-image-stackerA plugin designed to convert multiple open layers into a stack or vice versaThisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-image-stackerviapip:pip install napari-image-stackerTo install latest development version :pip install git+https://github.com/RobAnKo/napari-image-stacker.gitContributingContributions are very welcome. Tests can be run withtox.LicenseDistributed under the terms of theBSD-3license,
"napari-image-stacker" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-imaris-loader
DescriptionThis plugin enables viewing of Bitplane Imaris files, including very large datasets.  The GIFs below demonstrate rendering of a ~2TB IMS file containing a 2 color whole mouse brain.  The plugin has been tested on datasets as large as 20TB.NOTE: For this plugin to work "File/Preferences/Experimental/Render Images Asynchronously" must be selected.Open IMS file:Render in 3D:A plugin is provided to dynamically reload the data after selecting the lowest resolution level to be included in the viewer.  Since napari only renders the lowest resolution, the user can use this plugin to control the quality of 3D rendering.  See features and limitations for tips on suggested usage.FeaturesMultiscale RenderingImage pyramids which are present in the native IMS format are automatically added to napari during file loading.Chunks are implemented by dask and matched to the chunk sizes stored in each dataset.  (Napari appears to only ask for 2D chunks - unclear how helpful this feature is currently)Successfully handles multi-terabyte multi-timepoint multi-channel datasets.Tested with all sample files provided by Bitplane.Higher 3D rendering quality is enabled by a widget that reloads data after specifying the lowest resolution level (higher number = lower resolution) to be included in the multiscale series.Known Issues / limitationsCurrently, this isonly an image loader, and there are no features for loading or viewing objectsNapari sometimes throws errors indicating that it expected a 3D or 5D array but receives the other.This sometimesbut relatively rarelycauses napari to crashWould like to enable Asynchronous Tiling of Images, but this results in more instability and causes crashes.Thisnapariplugin was generated withCookiecutterusing with@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-imaris-loaderviapip:pip install napari-imaris-loaderChange Log:v0.1.2:Fixed:Issue where .ims files containing a single color 2D image would not open.Fixed:Issue where using the widget to change resolutions while in 3D rendering would cause a crash.  Now the viewer is automatically forced into 2D rendering mode when the widget is used.Dependency change:The loader is now dependent in a separate package for loading IMS files.https://pypi.org/project/imaris-ims-file-reader/v0.1.3:Documentationv0.1.4:Add napari to install requirements for plugin compatibilityv0.1.5:Changes to napari:now requires napari[all] upon install.requires >=v0.1.5 of imaris-ims-file-readerv0.1.6:Fix issue #7 where contrastLimits possibly unbound in readerv0.1.7:For squeeze_output=False when opening .ims file for Napari compatibilityv0.1.8:Add automatic determination of contrast_limitsFix bug in squeeze_outputContributingContributions 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-imaris-loader" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-imc
napari-imcImaging Mass Cytometry (IMC) file type support for napariLoad panoramas and multi-channel acquisitions co-registered within the machine's coordinate system from Fluidigm TXT/MCD filesInstallationYou can install napari-imc viapip:pip install napari-imcAlternatively, you can install napari-imc viaconda:conda install -c conda-forge napari-imcFor example, to install napari and napari-imc in a fresh conda environment using pip:conda create -n napari-imc python=3.9
conda activate napari-imc
pip install "napari[all]" napari-imcUsageSimply open your Fluidigm TXT/MCD file using napari.AuthorsCreated and maintained by Jonas Windhagerjonas.windhager@uzh.chCitationPlease cite the following paper when using napari-imc in your work:Windhager J, Bodenmiller B, Eling N (2021). An end-to-end workflow for multiplexed image processing and analysis. bioRxiv. doi:https://doi.org/10.1101/2021.11.12.468357.@article{Windhager2021,
  author = {Windhager, Jonas and Bodenmiller, Bernd and Eling, Nils},
  title = {An end-to-end workflow for multiplexed image processing and analysis},
  year = {2021},
  doi = {10.1101/2021.11.12.468357},
  URL = {https://www.biorxiv.org/content/early/2021/11/13/2021.11.12.468357},
  journal = {bioRxiv}
}ContributingContributingChangelogChangelogLicenseMIT
Package: napari-imsmicrolink
napari-imsmicrolinknapariplugin to perform MALDI IMS - microscopy registration using laser ablation marks as described inAnal. Chem. 2018, 90, 21, 12395–12403. This plugin is a work-in-progress but is mostly functional.N.B.This tool isNOTa general purpose registration framework to find transforms between IMS (MALDI or otherwise)
and microscopy. It is built to align MALDI IMS pixels to their corresponding laser ablation marks as captured by microscopy AFTER the IMS experiment.
This approach has the advantage of providing direct evidence of registration performance as IMS pixels are aligned
to theirexplicit spatial originin microscopy space, improving overall accuracy and confidence of microscopy-driven IMS
data analysis.InstallationYou can installnapari-imsmicrolinkviapip:pip install napari-imsmicrolinkTypical experiment workflowAcquire pre-IMS microscopy (autofluorescence, brightfield) -optionalPerform normal IMS sample preparation.Acquire post-IMS microscopy (autofluorescence, brightfield) with matrix still on sample
that reveals laser ablation marks.Gather IMS data that contains XY integer coordinates for the IMS experiment
(.imzML, Bruker spotlist (.txt, .csv), Bruker peaks.sqlite (FTICR),
Bruker .tsf (TIMS qTOF only))Runnapari-imsmicrolinkwith data 3 and 4Once registered, usewsiregto align other microscopy modalities to IMS-registered post-IMS
microscopyThisnapariplugin was generated withCookiecutterusing with@napari'scookiecutter-napari-plugintemplate.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-imsmicrolink" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.