Saravanan666/pypi-org huggingface dataset:
Package: napari-spatialdata
napari-spatialdata: interactive exploration and annotation of spatial omics dataThis repository contains a napari plugin for interactively exploring and annotating SpatialData objects.napari-spatialdatais part of theSpatialDataecosystem. To learn more about SpatialData, please see thedocumentation.InstallationYou can installnapari-spatialdataviapip:pip install napari-spatialdata[extra]Theextracommand will install the qt bindingsPyQt5.Note: if you have an M1/M2 Mac then you may get an error when installingPyQt5viapip. A solution is to first installnaparivia conda (which will correctly installPyQt5), usingmamba install -c conda-forge napari pyqtand then installnapari-spatialdataviapip, but without theextraoption:pip install napari-spatialdataYou can find more details on this in theinstallation instructions.Using napari-spatialdata as default zarr readerIf you would like to use the plugin as the default zarr reader, in napari please go toFile->Preferences->Pluginsand follow the instructions underFile extension readers.Development VersionYou can installnapari-spatialdatafrom Github with:pip install git+https://github.com/scverse/napari-spatialdataOr, you can also install in editable mode after cloning the repo by:git clone https://github.com/scverse/napari-spatialdata
cd napari-spatialdata
pip install -e .Note: when performing an editable install ofnapari-spatialdata,spatialdatawill be reinstalled frompip. So, if you previously also made an editable install ofspatialdata, you need to re-runpip install -e .on thespatialdatarepository. Please find more details on this in theinstallation instructions.Getting startedTo learn how to use thenapari-spatialdataplugin, please see thedocumentation. To learn how to integrate napari-spatialdata into your analysis workflows, please see theSpatialData tutorials. In particular:Annotating regions of interest with napariUse landmark annotations to align multiple -omics layersContributingContributions 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-spatialdata" is free and open source softwareIssuesIf you encounter any problems, please file anissuealong with a detailed description.
Package: napari-spatial-omics
napari-spatial-omicsA simple plugin to visualize spatial omic data stored in CSV formatThisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-spatial-omicsviapip:pip install napari-spatial-omicsTo install latest development version :pip install git+https://github.com/sebgoti/napari-spatial-omics.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-spatial-omics" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-sphinx-theme
napari-sphinx-themeA Sphinx theme based on the awesomepydata-sphinx-themewith the
look and feel of napari.This is currently a work-in-progress, but since it extends the
pydata-sphinx-theme, all the existing configurations and affordances are already
available. Check out thePyData Docsfor more
info.Installing for developmentAfter creating a virtual environment, install the theme in editable mode:python-mpipinstall-e.Building a demo siteTo build the demo site, run:cddocs/
makehtmlUsing it to build the napari websiteTo build the napari website, install the theme as a dependency.
Package: napari-splinedist
napari-splinedistA napari SplineDist pluginThisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-splinedistviapip:pip install napari-splinedistTo install latest development version :pip install git+https://github.com/DerThorsten/napari-splinedist.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-splinedist" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-splineit
napari-splineitA napari plugin for the interactive manipulation of spline-interpolation based geometrical modelsThisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-splineitviapip:pip install napari-splineitTo install latest development version :pip install git+https://github.com/uhlmanngroup/napari-splineit.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-splineit" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-spotiflow
napari-spotiflowNapari plugin forSpotiflow, a deep learning-based, threshold-agnostic, and subpixel-accurate spot detection method for fluorescence microscopy. For the main repo, seehere.https://github.com/weigertlab/napari-spotiflow/assets/11042162/02940480-daa9-4a21-8cf5-ad73c26c9838If you use this plugin for your research, pleasecite us.UsageOpen the image (or open one of our samples,e.g.File > Open Sample > napari-spotiflow > HybISS)Start the pluginPlugins > napari-spotiflowSelect model (pretrained or custom trained) and optionally adjust any other parametersClickrunSupported input formats2D (YX, YXC or CYX)2D+t (TYX, TYXC or TCYX)InstallationThe plugin can be installed directly from PyPi (make sure you use a conda environment withnapariandspotiflowinstalled):pip install napari-spotiflow
Package: napari-spreadsheet
napari-spreadsheetLet's replace Microsoft Excel or Google Spreadsheet withnapari-spreadsheetfor your daily image analysis.HighlightsConvert layer features to a spreadsheet.Update layer features from a spreadsheet.Send spreadsheet data to the namespace of napari's console directly.This plugin is largely dependent ontabulous. To know more about the user interface, please see thedocumentation.Thisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-spreadsheetviapip:pip install napari-spreadsheetTo install latest development version :pip install git+https://github.com/hanjinliu/napari-spreadsheet.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-spreadsheet" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-stable-diffusion
napari-stable-diffusionA demo of stable diffusion in napari.Thisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-stable-diffusionviapip:pip install napari-stable-diffusionTo install latest development version :pip install git+https://github.com/kephale/napari-stable-diffusion.gitYou will also need to sign up with HuggingFace andgenerate an access
tokento get access to the
Stable Diffusion model we use.When you have generated your access token you can either permanently
set theHF_TOKEN_SDenvironment variable in your.bashrcor whichever file
your OS uses, or you can include it on the command lineHF_TOKEN_SD="hf_aaaAaaaasdadsadsaoaoaoasoidijo" napariFor more information on the Stable Diffusion model itself, please seehttps://huggingface.co/CompVis/stable-diffusion-v1-4.Apple M1 specific instructionsTo utilize the M1 GPU, the nightly version of PyTorch needs to be
installed. Consider usingcondaormambalike this:mamba create -c pytorch-nightly -n napari-stable-diffusion python=3.9 pip pyqt pytorch torchvision
pip install git+https://github.com/kephale/napari-stable-diffusion.gitNext stepsImage 2 Image supportInpainting supportContributingContributions 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-stable-diffusion" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-stpt
napari-stptA napari viewer which reads stpt images as zarr files.Installation WindowsStart -> Anaconda3 (64-bit) -> Anaconda Prompt (Anaconda3)Type:>conda create -n py37 python=3.7

>conda activate py37

>pip install napari-stpt --upgradeInstallation LinuxApplications -> Terminal EmulatorType:>pip install napari-stpt --upgradeHow to runThe napari viewer can be run from command line by typing:>napari-stptHow to useIf working within the IMAXT Windows VMware or Linux remote desktop, the Data folder containing the STPT images will have been automatically selected (windows server: N:/stpt/; linux: /data/meds1_c/storage/processed/stpt). If not, please select the location of the folders with STPT Zarr files using the "Set folder" button.The dropdown box should now have all the available STPT images.Select the image file from the dropdown box.2D rendering (slice view)Select the slice you wish to view using the scroll bar.Press the "Load slice" button to load the image.When zooming using the mouse wheel the resolution will update dynamically.3D renderingThe "Output pixel size" is the resolution to which the images are reformatted (after applying the translations based on the bead locations).The "Maximum number of optical slices" can be set in case the optical slices go beyond the slice thickness of 15um. For example, if we have 9 optical slices of 2um we should use only 7 slices.Select which channels to load.Press "Load image 3D".To crop the volume draw a shape using the add rectangles button of napari. To do this select the "New shapes layer" button and then "Add rectangles" button. Draw a box across the image according to the region you wish to crop.Pressing "Crop to shape" will just crop the colume to this region.Pressing "Reload in shape" will reload the slices. In this case you can set a different output pixel size. To get the full resolution use a value of 0.5, although a value of 1 or 2 will in most cases suffice. Be aware that due to the limited memory the region will have to be rather small if the resolution increases.Press "Save volume" to save the multi-channel volume to a tiff file.Press the "Toggle number of display dimensions" button at the botton left (or press Ctrl-Y) to see the volume in 3D.Bead removalRemoving the beads requires a "Tissue threshold value" to be set which separates the tissue from background. Move the mouse over the image to get an idea of the values, which are shown in the status bar. There are two ways to remove the beads in a volume:Press button "Show only large regions" to remove all but the largest regions. The number of regions to retain can be selected for this.Press button "Remove small regions" to remove all the regions smaller than the size as defined by the "Minimum size".
Package: napari-stracking
napari-strackingnapari-strackingis a suite ofNapariplugins for thestracking librarydedicated to particles tracking in 2D+t and 3D+t images. Each step of
the tracking process is separated in independent plugins to ease the creation of pipelines.Thisnapariplugin was generated withCookiecutterusing with@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-strackingviapip:pip install napari-strackingContributingContributions 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-stracking" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-stress
napari-stressThis plugin provides tools for the analysis of surfaces in Napari, such as utilities to determine and refine the surface-representation of objects using a ray-casting approach and calculate the curvature of surfaces.
It re-implements code in Napari that was written forGross et al. (2021): STRESS, an automated geometrical characterization of deformable particles for in vivo measurements of cell and tissue mechanical stressesand has been made open source inthis repository.UsageFor documentation on how to use napari-stress both interactively from the napari-viewer or from code, please visit thedocumentationInstallationCreate a new conda environment with the following command.
If you have never used conda before, pleaseread this guide first.conda create -n napari-stress Python=3.9 napari jupyterlab -c conda-forge
conda activate napari-stressYou can then install napari-stress using pip:pip install napari-stressIssuesTo report bugs, request new features or get in touch, pleaseopen an issueor tag@EL_Pollo_Diabloonimage.sc.See alsoThere are other napari plugins with similar / overlapping functionalitymorphometricsnapari-pymeshlabnapari-process-points-and-surfacesContributingContributions 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-stress" is free and open source softwareAcknowledgementsThis project was supported by the Deutsche Forschungsgemeinschaft under Germany’s Excellence Strategy – EXC2068 - Cluster of Excellence "Physics of Life" of TU Dresden.
Package: napari-subboxer
napari-subboxerA napari plugin for visualising and interacting with electron cryotomograms.InstallationYou can installnapari-subboxerviapip:pip install napari-subboxerUsageThis plugin provides a user interface for opening electron cryotomograms in
napari as both volumes and slices through volumes.The plugin can be opened from thepluginsmenu in napari, or withnapari-subboxerat the command line.Usage:napari-subboxer [TOMOGRAM_FILE]An interactive tool for defining and applying relative transformson sets of particles in napari.Arguments:[TOMOGRAM_FILE]Options:--help                          Show this message and exit.ContributingContributions are very welcome.LicenseDistributed under the terms of theBSD-3license,
"napari-subboxer" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-superres
napari-superresA collection of super-resolution microscopy FF-SRM methods.Open-source implementation of methods for Fluorescence Fluctuation based Super Resolution Microscopy (FF-SRM):Review:Alva et al., 2022. “Fluorescence Fluctuation-Based Super-Resolution Microscopy: Basic Concepts for an Easy Start.” Journal of Microscopy, August.MSSR article:Torres-García, E., Pinto-Cámara, R., Linares, A. et al. Extending resolution within a single imaging frame. Nat Commun 13, 7452 (2022).ESI article:Idir Yahiatene, Simon Hennig, Marcel Müller, Thomas Huser (2015/2016). "Entropy-based Super-resolution Imaging (ESI): From Disorder to Fine Detail" ACS Photonics 8, 2 (2015)SOFI article:T. Dertinger, R. Colyer, G. Iyer, and J. Enderlein. Fast, background-free, 3D super-resolution optical fluctuation imaging (SOFI). PNAS 52, 106 (2009)SRRF article:Gustafsson, N., Culley, S., Ashdown, G., D. M. Owen, P. Matos Pereira, and R. Henriques. Fast live-cell conventional fluorophore nanoscopy with ImageJ through super-resolution radial fluctuations. Nat Commun 7, 12471 (2016)MUSICAL article:K. Agarwal and R. Machan, Multiple Signal Classification Algorithm for super-resolution fluorescence microscopy, Nature Communications, vol. 7, article id. 13752, (2016)Methods implemented:MSSRESISOFISRRFMUSICALSplit channelsSuper Resolution Radial Fluctuations (SRRF)Mean-Shift Super Resolution (MSSR)Entropy-based Super-resolution Imaging (ESI)from Fig. 7 ofAlva et al., 2022from Fig. 2 ofGarcía et al., 2021from Fig. 6 ofAlva et al., 2022Repositories available:ESIGitHub repositoryPySOFIGitHub repositoryMUSICALGoogle siteThisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.InstallationFirst install napari viewer (if you haven't):conda create -y -n napari-env -c conda-forge python=3.9
conda activate napari-env
pip install "napari[all]"For details check:https://napari.org/stable/You can install the plugingraphically.or install latest development version :pip install git+https://github.com/RoccoDAnt/napari-superres.gitYou might need to installgitfirst.Examples of use:OriginaltMSSRParameters:Amplification: 2, Order: 0, PSF FWHM: 6,Interpolation: Bicubic, Statistical integration: CV*sigmaOriginalESIParameters:image in output: 2, bins: 2, Order: 2OriginalSOFIParameters:Amplification factor: 2, Moment Order: 4, lambda parameter: 1.5, No. Iterations: 20, Window size: 100OriginalSRRFParameters:Amplification: 2, Spatial radius: 5, Symmetry Axis: 6, Start frame: 0, End frame: 48OriginalMUSICALParameters:Emission [nm]: 510 NA: 1.4, Mag: 100, Pizel size: 8000, Threshold: -0.5, Alpha: 4, Subpixels per pixel: 20ContributingContributions 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-superres" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-svetlana
napari_svetlanaThe aim of this plugin is to classify the output of a segmentation algorithm.
The inputs are :A folder of raw imagesTheir segmentation masks where each ROI has its own label.Svetlana can process 2D, 3D and multichannel image. If you want to use it to work on cell images, we strongly
recommend the use ofCellposefor the segmentation part, as it provides excellent quality results and a standard output format
accepted by Svetlana (labels masks).If you use this plugin please cite thepaper:Cazorla, C., Weiss, P., & Morin, R. (2023). Svetlana: a Supervised Segmentation Classifier for Napari.@unpublished{weiss:hal-03927879,TITLE={{Svetlana: a Supervised Segmentation Classifier for Napari}},AUTHOR={Weiss, Pierre and Cazorla, Cl{\'e}ment and Morin, Renaud},URL={https://hal.inria.fr/hal-03927879},NOTE={working paper or preprint},YEAR={2023},MONTH=Jan,PDF={https://hal.inria.fr/hal-03927879/file/main_nature.pdf},HAL_ID={hal-03927879},HAL_VERSION={v1},}Thisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.InstallationFirst install Napari in a Python 3.9 Conda environment following these instructions :condacreate-nsvetlana_envpython=3.9
condaactivatesvetlana_env
condainstallpip
python-mpipinstall"napari[all]"==0.4.17Then, you can installnapari_svetlanaviapip, or directly from the Napari plugin manager (see Napari documentation):pipinstallnapari_svetlanaWARNING:If you have a Cuda compatible GPU on your computer, some computations may be accelerated
usingCupy. Unfortunately, Cupy needs Cudatoolkit to be installed. This library can only be installed via
Conda while the plugin is a pip plugin, so it must be installed manually for the moment:condainstallcudatoolkit=10.2Also note that the library (Cucim) that we use to improve these performances, computing morphological operations on GPU
is unfortunately only available for Linux systems. Hence, if you are a Windows user, this installation is not necessary.TutorialMany advanced features are available in Svetlana, such as data augmentation or contextual information reduction, to optimize the performance of your classifier. Thus, we strongly encourage you to
check ourYoutube tutorialand
ourdocumentation.
A button calledTRY ON DEMO IMAGEis available in the annotation plugin and enables you to apply the YouTube
tutorial to the same test images to learn how to use the plugin. Feel free to try it to test all the features
that Svetlana offers.Similar Napari pluginsJoel Luethi developed a similar method for objects classification callednapari feature classifier.
Also,apocby Robert Haase is available in Napari for pixels and objects classification.ContributingContributions are very welcome.LicenseDistributed under the terms of theBSD-3license,
"napari_svetlana" is free and open source softwareAcknowledgementsThe method was developed byClément Cazorla,Renaud MorinandPierre Weiss. And the plugin was written by
Clément Cazorla. The project is co-funded byImactiv-3DandCNRS.IssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-svg
napari-svgA plugin for reading and writing svg files with napariThisnapariplugin was generated withCookiecutterusing with@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-svgviapip:pip install napari-svgContributingContributions 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-svg" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-tabu
napari-tabuA plugin for handling multiple napari windowsUsageTo open a new window, first click the menuPlugins > napari-tabu: open new windowAfterwards, select the layer which should be opened in the new window and click onRun:When you're done with working with the new window, you can send back the result of your work using theSend current layer back to main napaributoon:Thisnapariplugin was generated withCookiecutterusing with@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-tabuviapip:pip install napari-tabuContributingContributions 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-tabu" is free and open source softwareIssuesIf you encounter any problems, please open a thread onimage.scalong with a detailed description and tag@haesleinhuepf.
Package: napari-text-layer
napari-text-layerNapari text layer for bio-image annotation.InstallationYou can install using pip:pip install napari-text-layerKeybindings and mouse callbacks"→", "←", "↑", "↓" ... Move selected shapes by 1 pixel."F2" ... Enter edit mode at the selected shape (or the last one if no shape is selected)."Enter" ... Finish edit mode or add a new shape at the same interval."Ctrl" + "Shift" + "<" or ">" ... Change font size.double click ... Enter edit mode at the clicked shape.
Package: napari-threedee
napari-threedeeA suite of useful tools based on 3D interactivity in napariThisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-threedeeviapip:pip install napari-threedeeTo install latest development version :pip install git+https://github.com/alisterburt/napari-threedee.gitExample applicationsSee the full list ofexample gallery scripts here on our website.mesh lighting controlannotate points on planesrender plane manipulatorlayer manipulatorpoint manipulatorContributingContributions 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-threedee" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-tiff
napari-tiffA napari plugin for tiff images.Thisnapariplugin was generated withCookiecutterusing with@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-tiffviapip:pip install napari-tiffContributingContributions 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-tiff" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.