Saravanan666/pypi-org huggingface dataset:
Package: napari-lazy-openslide
napari-lazy-openslideAn experimental plugin to lazily load multiscale whole-slide tiff images with openslide and dask.Thisnapariplugin was generated withCookiecutterusing with@napari'scookiecutter-napari-plugintemplate.InstallationStep 1.)Make sure you have OpenSlide installed. Download instructionshere.NOTE: Installation on macOS is easiest via Homebrew:brew install openslide. Up-to-date and multiplatform
binaries foropenslideare also avaiable viaconda:conda install -c sdvillal openslide-pythonStep 2.)Installnapari-lazy-openslideviapip:pip install napari-lazy-openslideUsageNapari plugin$naparitumor_004.tifBy installing this package viapip, the plugin should be recognized bynapari. The plugin
attempts to read image formats recognized byopenslidethat are multiscale
(openslide.OpenSlide.level_count > 1).It should be noted thatnapari-lazy-openslideis experimental and has primarily
been tested withCAMELYON16andCAMELYON17datasets, which can be
downloadedhere.UsingOpenSlideStorewith Zarr and DaskTheOpenSlideStoreclass wraps anopenslide.OpenSlideobject as a valid Zarr store.
The underlyingopenslideimage pyramid is translated to the Zarr multiscales extension,
where each level of the pyramid is a separate 3Dzarr.Arraywith shape(y, x, 4).importdask.arrayasdaimportzarrfromnapari_lazy_openslideimportOpenSlideStorestore=OpenSlideStore('tumor_004.tif')grp=zarr.open(store,mode="r")# The OpenSlideStore implements the multiscales extension# https://forum.image.sc/t/multiscale-arrays-v0-1/37930datasets=grp.attrs["multiscales"][0]["datasets"]pyramid=[grp.get(d["path"])fordindatasets]print(pyramid)# [#   <zarr.core.Array '/0' (23705, 29879, 4) uint8 read-only>,#   <zarr.core.Array '/1' (5926, 7469, 4) uint8 read-only>,#   <zarr.core.Array '/2' (2963, 3734, 4) uint8 read-only>,# ]pyramid=[da.from_zarr(store,component=d["path"])fordindatasets]print(pyramid)# [#   dask.array<from-zarr, shape=(23705, 29879, 4), dtype=uint8, chunksize=(512, 512, 4), chunktype=numpy.ndarray>,#   dask.array<from-zarr, shape=(5926, 7469, 4), dtype=uint8, chunksize=(512, 512, 4), chunktype=numpy.ndarray>,#   dask.array<from-zarr, shape=(2963, 3734, 4), dtype=uint8, chunksize=(512, 512, 4), chunktype=numpy.ndarray>,# ]# Now you can use numpy-like indexing with openslide, reading data into memory lazily!low_res=pyramid[-1][:]region=pyramid[0][y_start:y_end,x_start:x_end]ContributingContributions are very welcome. Tests can be run withtox, please ensure
the coverage at least stays the same before you submit a pull request.IssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-listener
napari-listenerOpens a socket to listen for commands to control napari from other processes.
This can be useful for controlling napari programmatically from other
applications, or for improving general OS integration (e.g. opening data from a
file or UrL in a running instance of napari).Thisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-listenerviapip:pip install napari-listenerUsageOnce installed,napari-listenercan be started from thenapari > Plugins > Start Listeningmenu. You will see a new docked widget that displays the
address and port for the listener.The listener is a TCP server that expects app-model command IDs. It will
execute any valid app-model command, butnapari-listenerregisters its own
additional commands for demonstration purposes inhttps://github.com/aganders3/napari-listener/blob/main/src/napari_listener/_actions.py.You can testnapari-listenerusing a TCP client such asnetcatorcurlto send an app-model command (and
optional args). For example:%nc127.0.0.140256<<<"napari:open-file /path/to/local/file"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-listener" is free and open source softwareIssuesIf you encounter any problems, please [file an issue] along with a detailed
description.
Package: napari-live-flim
napari-live-flimA plugin for real-time FLIM analysisThisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.Required dependenciesOpenScanTCSPC module and all dependencies.Verify FLIM electronics are compatible with OpenScanPython and thenaparipackage and all dependenciesYou can installnapariviapip:pip install napari[all]InstallationYou can installnapari-live-flimviapip:pip install napari-live-flimUsageIn MicroManager, set a port number in the device property setting namedOpenScanFLIM-BH-TCSPC-SendFLIMHistogramsToUDPPortIn Napari, selectPlugins > FLIM Viewer (napari-live-flim)to run the plugin. Enter the same port number to connect to OpenScan.Begin acquisition within MicroManager.Interact with the FLIM data in real-time within napari.Modify the FLIM Parameters and Display Filters settings as desired.Add selections to the Lifetime Image or Phasor Plot by clicking the relevant New Selection buttons.Manipulate the selections with the mouse cursor and modify the selection layer with the layer controls.Click the Snapshot button during acquisition to take a snapshot.Use the scroll bar under the Lifetime Image to recall a specific snapshot.Stop scanning within MicroManager to end acquisition.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 theGNU GPL v3.0license,
"napari-live-flim" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-live-histogram
napari-live-histogramDisplay the image histogram in Napari. The histogram is updated live if the selected layer data changes, for example if image data is being streamed from a camera.InstallationYou can installnapari-live-histogramviapip:pip install napari-live-histogramUsageSelect the plugin from thePluginsmenu of Napari.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-live-histogram" 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-live-recording
napari-live-recordingA napari plugin for live video recording with a generic camera device and generate a stack of TIFF images from said device.The plugin provides a common interface for a generic camera device to be directly controlled from the napari GUI. The plugin canacquire continously in live view;record a stack of images and store them as ImageJ-compatible TIFF, OME-TIFF or HDF5 files.Thisnapariplugin was generated withCookiecutterusing with@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-live-recordingviapip:pip install napari-live-recordingIf you want to install the plugin using the source code, you can do so by cloning the project and installing locally:git clone https://github.com/jacopoabramo/napari-live-recording
cd napari-live-recording
pip install .DocumentationYou can review the documentation of this pluginhereContributingContributions 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-live-recording" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-locan
napari-locanLoad, visualize and analyze single-molecule localization microscopy (SMLM) data.napari-locan is a napari plugin that implements a subset of methods fromlocan,
a python-based library with code for analyzing SMLM data.
Locan provides extended functionality that is better suited for script- or
notebook-based analysis procedures.
napari-locan is well suited for exploratory data analysis within napari.For details on usage and development of napari-locan please read thedocumentation.InstallationMake sure to have Qt bindings installed in your python environment of choice.You can install napari-locan from PyPI:pip install napari-locanor from conda-forge:mamba install -c conda-forge napari-locanPlease read thedocumentation on installationfor more details.UsagePlease read thedocumentationfor details.ContributingContributions are very welcome.
Please read thedocumentation on developmentfor details.CreditThe plugin was developed in the Department of Biotechnology and Biophysics,
Würzburg University, Germany.
It is based on locan. So credit goes to thelocan developersand can becited.LicenseDistributed under the terms of theBSD-3license, "napari-locan" is free and open source software.
See theLICENSEfile for details.IssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.Thisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.
Package: napari-locpix
napari-locpixLoad in SMLM data and annotate within napariThisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-locpixviapip:pip install napari-locpixTo install latest development version :pip install git+https://github.com/oubino/napari-locpix.gitUsageThis plugin allows a user toRead in SMLM dataVisualise SMLM data in a histogramAdd segmentations to the dataExtract the underlying localisations from the segmentationsIOThe input data can be in the form of a .csv or .parquet.We expect there to be 4 columns at least, which should he identified inthe file column selection:X coordinateY coordinateFrameChannelIf the data has been annotated with this software we can also load this in.
Note however we currently only support loading in annotated data saved as a .parquet folder.
Therefore, we recommend always keeping a .parquet copy until loading in an annotated .csv
is supported.The data can be outputted to a .parquet or a .csvDrop localisations with zero label, gives you the option to only save the localisations which have been annotated i.e. labels 1 and above.Channels labels allows you to give a real name label to each of the channels e.g. Chan 0 label: 'Alexa 647'VisualisationUsing the render button you can render the loaded in data according to the histogram settingsX/Y bins defines the number of bins for the histogramVis interpolation defines how to interpolate the image before viewingAnnotationsAnnotations can be added using Napari's viewer.Simply click the add Labels.Note that this software will expect the labels to be called "Labels"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-locpix" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-magic-wand
🪄 napari-magic-wandObject annotation in Napari usingmagic wands(shortest path algorithms). This plugin supports annotation in 2D (grayscale and RGB), 2D+t (grayscale, frame by frame) and 3D images (slice by slice). It can be used to annotatepathsor the contour of solid objects.The plugin provides two annotation functions:TheMagic wandtool is based on thePyIFTlibrary. Use it to trace annotations that follow theintensity gradientsin the image.TheBrightest pathtool is based on theBrightest Path Liblibrary. Use it to trace annotations that followthe brightest (or darkest) pathbetween two points.Related pluginsTake a look at these related plugins that offer similar functionality and slightly different user interactions.grabber-iftwhich is based onpyift.napari-tracingwhich is based onbrightest-path-lib.InstallationYou can installnapari-magic-wandviapip:pip install napari-magic-wandUsageSelect the tool of your choice from thePluginsmenu of Napari.Open an image to annotate (2D, 2D+t, or 3D).Click on the button "Start live wire". A newLabelslayerLive wire (current edit)should appear.Click on the image to annotate paths interactively.Double-click to confirm an annotation and move to the next.Options and parametersClose and fill objects: You can fill (or not) the inside of the annotated object. Do not tick this option if you are annotatingpaths(e.g. filament-like strucutres).Auto-increment label index: Tick this option to increment the label index every time a new object is completed (e.g. if you are annotating multiple objects).Sigma: Higher values of sigma increase the "stickiness" of the object boundaries to the magic wand.Black ridges: Tick this checkbox if you are annotating dark paths on a bright background.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-magic-wand" 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-mahotas-image-processing
Note: This is a decommissioned napari pluginThis project is discontinued. You can still install and use it (version 0.1.2 was last tested with napari 0.4.12) but this project is
no longer maintained and supported.condainstallpyopenclpipinstallnapari-mahotas-image-processing==0.1.2Check out these napari plugins which have similar functionality:napari-zeldanapari-allencell-segmenternapari-simpleitk-image-processingnapari-segment-blobs-and-things-with-membranesnapari_pyclesperanto_assistantnapari-mahotas-image-processing (n-mahotas)Image processing based using theMahotas libraryinnapariUsageGaussian blurApplies aGaussian blurto an
image. This might be useful for denoising, e.g. before applying the Threshold-Otsu method.Otsu's thresholdBinarizes an image usingscikit-image's threshold Otsu algorithm, also known asOtsu's method.Split connected objectsIn case objects stick together after thresholding, this tool might help.
It aims to deliver similar results asImageJ's watershed implementation.Connected component labelingTakes a binary image and produces a label image with all separated objects labeled differently. Under the hood, it usesmahotas' label function.Seeded watershedStarting from an image showing high-intensity membranes and a seed-image where objects have been labeled,
objects are labeled that are constrained by the membranes. Hint: you may want to blur the membrane channel a bit in advance.Thisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.InstallationBefore installing this napari plugin, pleaseinstallmahotas, e.g. using conda:conda config --add channels conda-forge
conda install mahotasAfterwards, you can installnapari-mahotas-image-processingviapip:pip install napari-mahotas-image-processingTo install latest development version :pip install git+https://github.com/haesleinhuepf/napari-mahotas-image-processing.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-mahotas-image-processing" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-manual-classifier
napari-manual-classifierSimple napari widget for annotating classes for each slice of an nd-imageThisnapariplugin was generated withCookiecutterusing with@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-manual-classifierviapip:pip install napari-manual-classifierContributingContributions 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-manual-classifier" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-manual-split-and-merge-labels
This is a decommissioned napari plugin. The code has been moved tonapari-segment-blobs-and-things-with-membranes.You can still install this plugin to napari as described below. It was last tested with napari 0.4.11.napari-manual-split-and-merge-labelsSplit and merge labels in napari manuallyThisnapariplugin was generated withCookiecutterusing with@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-manual-split-and-merge-labelsviapip:pip install napari-manual-split-and-merge-labels==0.1.3ContributingContributions 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-manual-split-and-merge-labels" 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-manual-transforms
napari-manual-transformsInterface to manually edit layer affine transforms.express rotations as quaternion, euler angle, or axis + angle.allows rotation around arbitrary origincurrently, focusing on rigid rotationsAlt-Drag to rotate a layer independently of the rest.image resampling (i.e. "apply" the transformation to create new dataset that can be saved)caveats:only works on 3D Image layers for now, open a feature request for other dims/layers.will likely result in "Non-orthogonal slicing is being requested" warnings in 2D view.Try it outimportnapariv=napari.Viewer()v.dims.ndisplay=3v.open_sample('napari','cells3d')v.window.add_plugin_dock_widget('napari-manual-transforms')napari.run()InstallationYou can installnapari-manual-transformsviapip:pipinstallnapari-manual-transformsTo install latest development version :pipinstallgit+https://github.com/tlambert03/napari-manual-transforms.gitLicenseDistributed under the terms of theBSD-3license,
"napari-manual-transforms" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-mat-file-reader
napari-mat-file-readerThis is a simple wraper to read .mat files from MatlabThisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-mat-file-readerviapip:pip install napari-mat-file-readerTo install latest development version :pip install git+https://github.com/rjlopez2/napari-mat-file-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-mat-file-reader" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-math
napari-mathThis package provides a GUI interfrace for simple mathematical operations on image, point and surface layers.additionsubtractionmultiplicationdivisionlogical and, or, xorz-projection (mean and sum)Operations can be peformed on a single layer or between Image layers (functionaly pending for Surface and Point layers),
for example adding one layer to another.When performing operations on two images of different sizes, the result will be the size of the smallest
of the two images.InstallationYou can installnapari-mathviapip:pip install napari-mathContributingContributions 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-math" is free and open source softwareIssuesIf you encounter any problems, please file an [issue] along with a detailed description.
Package: napari-mat-images
napari-mat-imagesFeaturesThis plugin loads image variables stored inMATLAB.matfiles intonapari.It loads any variable that looks like an image.
Presently, that includes any array with more than two dimensions with size greater than 20 pixels (determined byshape_is_image()).If loading a variable with 3 or more dimensions, the plugin assumes that it is a stack of images, and the dimension with greatest size is the axis of the stack.Loading Large FilesIf loading a large.matfile saved inHDF5/v7.3format, chunks of the images are loaded as needed, resulting in fast initial load, but potentially slower scrolling.Slices of the image stacks are randomly sampled to determine min/max contrast values.RequirementsThis plugin relies onscipyto load small.matfiles andh5py(withdask) to load largerHDF5/v7.3.matfiles.It implicitly requiresnaparifor use.Installationnapari-mat-imagesrequiresnaparito be installed, although it is not listed as a requirement for installation.
This plugin relies on plugin functionality found innapariversion >0.2.12. This can be installed viapipfromPyPI:$ pip install napari>0.2.12You can installnapari-mat-imagesviapipfromPyPI:$ pip install napari-mat-imagesUsageOnce installed, the plugin will be used whenever trying to load a.matfile.
This can be done from thenapariGUI or commandline:$ napari my_file.matContributingContributions are very welcome.
Tests can be run withpytest,
please ensure the coverage at least stays the same before you submit a pull request.LicenseDistributed under the terms of theBSD-3license,napari-mat-imagesis free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.Thisnapariplugin was generated withCookiecutteralong withnapari'scookiecutter-napari-plugintemplate.
Package: napari-matplotlib
napari-matplotlibA plugin to create Matplotlib plots from napari layersIntroductionnapari-matplotlibis a bridge betweennapariandmatplotlib, making it easy to create publication qualityMatplotlibplots based on the data loaded innaparilayers.Documentaiton can be found athttps://napari-matplotlib.github.io/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-matplotlibis free and open source software.IssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.