Saravanan666/pypi-org huggingface dataset:
Package: napari-brainways
OverviewWhat Is Brainways?Brainways is an AI-based tool for automated registration, quantification and generation of brain-wide activity networks based on fluorescence in coronal slices.Why Brainways?Coronal slice registration, cell quantification and whole-brain contrast analysis between experimental conditions should be made easily accessible from a single software, without requiring programming experience.
Customization should be made easy by having a highly flexible pythonic backend.Getting StartedTo install and run brainways, run the following in your python environment:pipinstallnapari-brainways
napari-wnapari_brainwaysFollow ourgetting started guidefor more details.How it worksBrainways allows users to register, quantify and provide statistical contrast analysis by following several simple steps:Rigid registration of coronal slices to a 3D atlas.Non-rigid registration of coronal slices to a 3D atlas, to account for individual difference and imperfections in acquisition procedure.Cell detection (usingStarDist).Quantification of cell counts per brain region.Statistical analysis:ANOVA contrast analysis.PLS (Partial Least Square) analysis.Network graph creation.ArchitectureBrainways is implemented as three python packages.napari-brainwayscontains the GUI implementation as anapariplugin. napari-brainways is usingbrainwaysas its backend. All of the functionality is implemented in the brainways package. This separation was done to guarantee that brainways is a GUI-agnostic software, and can be fully accessed and manipulated through python code to allow custom complex usage scenarios. The code that was used to train, evaluate and run the automatic registration model resides inbrainways-reg-model.Development StatusBrainways is being actively developed by Ben Kantor of Bartal lab, Tel Aviv University, Israel. Our releases can be foundhere.CitationIf you use brainways, please citeKantor and Bartal (2023):@article{kantor2023brainways,
  title={Brainways: An Open-Source AI-based Software For Registration and Analysis of Fluorescent   Markers on Coronal Brain Slices},
  author={Kantor, Ben and Ben-Ami Bartal, Inbal},
  journal={bioRxiv},
  pages={2023--05},
  year={2023},
  publisher={Cold Spring Harbor Laboratory}
}LicenseDistributed under the terms of theGNU GPL v3.0license,
"napari-brainways" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-brightness-contrast
napari-brightness-contrastAdvanced layer histogram visualization options, e.g. for brightness / contrastNote: This will not work for big image data at the moment.
If the user interface feels slow, consider installingpyclesperantoto speed it up.Thisnapariplugin was generated withCookiecutterusing with@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-brightness-contrastviapip:pip install napari-brightness-contrastContributingContributions are very welcome.After cloning the repo, install usingpip install -e .[tests]to enable testing viapytest.LicenseDistributed under the terms of theBSD-3license,
"napari-brightness-contrast" is free and open source softwareIssuesIf you encounter any problems, pleaseopen a thread on image.scalong with a detailed description and tag@haesleinhuepf.
Package: napari-broadcastable-points
napari-broadcastable-pointsPoints layer that can broadcast over arbitrary dimensions. Available here as a workaround until something more complete is implemented in napari core (https://github.com/napari/napari/issues/2343).Warning!This is likely to be very brittle for all the reasons discussed in the napari issue - so while it is useful it should also be used with caution. So don't muck around much with the viewer dims after creating, because who knows what will happen.Installationpipinstallnapari-broadcastable-pointsUsageHere is an example where we have an  image sequence of (TPCZYX) and we broadcast points over theCandZaxes.importnaparifromnapari_broadcastable_pointsimportBroadcastablePointsimportnumpyasnpv=napari.Viewer()# create a fake timelapseT=5P=4C=3Z=2Y,X=512,512images=np.zeros([T,P,C,Z,Y,X])v.add_image(images)# Add the relevant components of points data# fmt: offdat=np.array([# T,  P,       Y,              X[0,0.,340.25071184,284.13186557],[0,0.,312.66551847,309.95630191],[0,0.,240.76794003,266.81775485],[0,0.,240.47448053,239.81948049],[0,1.,261.60356481,260.36164576],[0,1.,309.43746393,215.16888217],[0,1.,371.06395974,235.12412843]])# fmt: onv.dims.axis_labels=('T','P','C','Z','Y','X')points=BroadcastablePoints(dat,broadcast_dims=(2,3))v.add_layer(points)napari.run()Creating an empty layerYou can also create an empty layer - but be sure to specifyndimotherwise you may run into an error.points=BroadcastablePoints(None,broadcast_dims=(2,3),ndim=6)
Package: napari-brushsettings
napari-brushsettingsA simple plugin to set the brush settings for segmentation in napariThisnapariplugin was generated withCookiecutterusing with@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-brushsettingsviapip:pip install napari-brushsettingsContributingContributions 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-brushsettings" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-bud-cell-segmenter
napari-bud-cell-segmenterA plugin to segment embryonic mammary bud cells and detect 2 RNA probesThisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-bud-cell-segmenterviapip:pip install napari-bud-cell-segmenterTo install latest development version :pip install git+https://github.com/AurelienMaillot/napari-bud-cell-segmenter.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-bud-cell-segmenter" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-calibration
napari-calibrationPlug in which enables to make camera calibrationThisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-calibrationviapip:pip install napari-calibrationTo install latest development version :pip install git+https://github.com/tcotte/napari-calibration.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-calibration" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-caphid
napari-caphidAnnotation of aphid and update tableNapari-caphid was developed for updating table of quantitative data from images. Napari-caphid was developed by Imhorphen Team (french team of University of Angers and INRAe Angers) for ECLECTIC Team (french team of University of Paris-Saclay and CNRS).InstallationYou can installnapari-caphidviapip:pip install napari-caphidTo install latest development version :pip install git+https://github.com/hereariim/napari-caphid.gitGetting startedForewordBefore using the plugin, the directory must be structured as follows:└── Directory
    ├── France
    │   ├── image
    │   │   ├── img_1.tif
    │   │   ├── img_2.tif
    │   │   ...
    │   │   └── img_n.tif
    │   ├── mask
    │   │   ├── msk_1.tif
    │   │   ├── msk_2.tif
    │   │   ...
    │   │   └── msk_n.tif
    │   ├── img_1.tif
    │   ├── msk_1.tif
    │   ├── img_2.tif
    │   ├── msk_2.tif
    │   ...
    │   ├── img_n.tif
    │   └── msk_n.tif
    │ 
    ├── Belgium
    │   ├── image
    │   │   └── ...
    │   ├── mask
    │   │   └── ...
    │   └── ...
    ├── Spain
    │   ├── image
    │   │   └── ...
    │   ├── mask
    │   │   └── ...
    │   └── ...
    └── Aphid.csvSome explanation about structure. The directory contained three folders (France, Spain, Belgium) and one file (Aphid.csv).Each folders (France, Spain, Belgium) contains a set of images and masks and two folders (image, mask). The folder image contains images from the set of images. The folder mask contains masks from the set of masks.The file Aphid.csv is a table with quantitative data of aphids from inital process of aphid image processing.Important:The structure of directory is very important because it will be useful to get image name.Getting startedThe widget get three input:Mask : Mask stackPick a table : Path/to/Directory/Aphid.csvCountry : The country where images were takenThe widget gives one output:A new table .csv which is the Aphid.csv updated.What's it for ?This widget gives quantitative data from Mask stack. These quantitative data will be contained into dataframe. Quantitative data linked to current masks contained in the Aphid.csv file will be deleted. Then, the new quantitative data contained in the dataframe will be integrated into the Aphid.csv file. In this way, the Aphid.csv file is updated.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-caphid" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-ccp4map
napari-ccp4mapEnables napari to read .map files in the ccp4 format.Thisnapariplugin was generated withCookiecutterusing with@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-ccp4mapviapip:pip install napari-ccp4mapUsageIf the plugin was installed correctly, it will pop up in a napari window under Plugins->Install/Uninstall Plugins.
You can either drag&drop filed into the window to read them, or search for a folder/file using Ctrl+O.How it worksThis plugin simply reads a file and allowsgemmito interact with it. Then, numpy turns the file into an array.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-ccp4map" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-cell-centroid-annotator
napari-cell-centroid-annotatorA simple plugin to annotate cell centroids in 3D imagesThisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-cell-centroid-annotatorviapip:pip install napari-cell-centroid-annotatorTo install latest development version :pip install git+https://github.com/tim-vdl/napari-cell-centroid-annotator.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-cell-centroid-annotator" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-checkerboard
napari-checkerboardCompare two images with the itk checkerboard filterThisnapariplugin was generated withCookiecutterusing with@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-checkerboardviapip:pip install napari-checkerboardContributingContributions 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-checkerboard" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-clipboard
napari-clipboardA plugin for creating napari layers from the System clipboardThisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-clipboardviapip:pip install napari-clipboardTo install latest development version :pip install git+https://github.com/kephale/napari-clipboard.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-clipboard" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-conference
napari-conferenceA simple plugin that allows you to use napari + your webcam in video
callsUsagePlugins>start conferenceCheckrunningcheckboxPressUpdatebutton to update any setting (and start/stop)If things work in zoom but you don't show up, then make sureblur backgroundis disabled.InstallationPrerequisitesYou will need to:followpyvirtualcam's installation instructions:https://github.com/letmaik/pyvirtualcam#installationinstallnaparifrom source to get the new async slicing updatesNote: I needed to installpyvirtualcamfrom source on my MacOS M1
with python=3.10.[Not available on pypi yet] You can installnapari-conferenceviapip:pip install napari-conferenceTo install latest development version :pip install git+https://github.com/kephale/napari-conference.gitKnown Issuesresizing the napari window while streaming causes a crashcannot be restarted after stopping the widgetContributingContributions 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-conference" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.Thisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.
Package: napari-conidie
napari-conidieA segmentation tool to get conidie and hypheThisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.This plugin is a use case for obtaining conidia and hyphae surface from images. This plugin is a private tool dedicated exclusively to the work of the QUASAV team.InstallationThis private tool cannot be found in the built-in napari. The installation therefore follows two steps:1 - Install latest development version :git clone https://github.com/hereariim/napari-conidie.gitOr:Download napari-conidie zip file2 - Drag and drop napari-conidie file into the built-inContributingContributions 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-conidie" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-console
napari-console (WIP, under active development)A plugin that adds a console to napariThisnapariplugin was generated withCookiecutterusing with@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-consoleviapip:pip install napari-consoleContributingContributions 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-console" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-convpaint
napari-convpaintThis napari plugin can be used to segment objects in images based on a few brush strokes providing examples of foreground and background. Based on the same idea as other tools like ilastik, its main strength is that it provides good results without adjusting any parameters. The filters used to generate features for classification are indeed taken from layers of trained deep learning networks and don't need to be chosen manually. Find more information in thedocs.The idea behind the plugin comes directly from the work of Lucien Hinderling (University of Bern) and can be found here:https://github.com/hinderling/napari_pixel_classifier.InstallationYou can installnapari-convpaintviapippip install napari-convpaintTo install latest development version :pip install git+https://github.com/guiwitz/napari-convpaint.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-convpaint" is free and open source softwareContributingContributions are very welcome. Tests can be run withtox, please ensure
the coverage at least stays the same before you submit a pull request.AuthorsThe idea behind this napari plugin was first developed by Lucien Hinderling in the group ofOlivier Pertz, at the Institute of Cell Biology, University of Bern. The code has first been shared as open source resource in form of aJupyter Notebook. With the desire to make this resource accessible to a broader public in the scientific community, the Pertz lab obtained a CZI napari plugin development grant with the title"Democratizing Image Analysis with an Easy-to-Train Classifier"which supported the adaptation of the initial concept as a napari plugin called napari-convpaint. The plugin has been developed by Guillaume Witz, Mykhailo Vladymyrov and Ana Stojiljkovic at theData Science Lab, University of Bern, in tight collaboration with the Pertz lab.IssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-cookiecut
napari-cookiecutA fixed version of a cookiecut napari plugin template that has been set up with all the basic functionality following the README for reference.Thisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-cookiecutviapip:pip install napari-cookiecutTo install latest development version :pip install git+https://github.com/seankmartin/napari-cookiecut.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-cookiecut" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-correct-drift
napari-correct-driftNapari-correct-drift brings the functionality of Fiji’s popular Correct-3D-drift macro to Napari for flexible and efficient correction of stage and sample drift common in time-lapse microscopy.Napari-correct-drift supports drift correction for 2D/3D multi-channel data.Examplehttps://user-images.githubusercontent.com/895863/235100349-83379350-06a5-4fe7-9323-f3e5771cca2e.mp4Test dataNapari-correct-drift contains synthetic sample data. To test it on real data download an example Arabidopsis growingroot tipfile.InstallationYou can installnapari-correct-driftvia [pip]:pip install napari-correct-driftTo install latest development version :pip install git+https://github.com/sommerc/napari-correct-drift.gitRoadmapBasic CorrectDrift interfaceSynthetic test dataUnit tests2D/3D multi-channel supportROI support (rectangles)Saving and loading of drift tablesOutlier handlingSphinx documentationHow-tosTutorials and GuidesContributingContributions are very welcome. Tests can be run with [tox], please ensure
the coverage at least stays the same before you submit a pull request.LicenseDistributed under the terms of the [BSD-3] license,
"napari-correct-drift" is free and open source softwareAcknowledgmentThis project has been made possible in part by grant number NP2-0000000051 from the napari Plugin Foundations Grants (Cycle 2).
Package: napari-crop
napari-cropCrop regions in napari manuallyCrop in any dimensionCut a volume using a planeNote: this functionality currently only works with 3D dataUsageCreate a new shapes layer to annotate the region you would like to crop:Use the rectangle tool to annotate a region. Start thecroptool from theTools > Utilities > Crop regionmenu.
Click theRunbutton to crop the region.You can also use theSelect shapestool to move the rectangle to a new place and crop another region by clicking onRun.Hint: You can also use thenapari-tabuplugin to send all your cropped images to a new napari window.Thisnapariplugin was generated withCookiecutterusing with@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-cropviapip:pip install napari-cropContributingContributions are very welcome.LicenseDistributed under the terms of theBSD-3license,
"napari-crop" 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-cryofibsem-monitor
napari-cryofibsem-monitorA plugin to monitor the creation of lamella using AutoTEM on a TFS Acquilos instrumenthttps://user-images.githubusercontent.com/6081039/201448228-fdd8b429-8ff6-4934-ad58-e80fbfcbaef0.mp4Changelogv0.0.3Update data during millingAlign images to keep lamella in the centerMonitor thicknessThisnapariplugin was generated withCookiecutterusing with@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-cryofibsem-monitorviapip:pip install napari-cryofibsem-monitorTo install latest development version :pip install git+https://github.com/jojoelfe/napari-cryofibsem-monitor.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-cryofibsem-monitor" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-cupy-image-processing
napari-cupy-image-processingGPU-accelerated image processing usingcupyandCUDAUsageThis napari plugin adds some menu entries to the Tools menu. You can recognize them with their suffix(n-cupy)in brackets.
Furthermore, it can be used from thenapari-assistantgraphical user interface.
Therefore, just click the menuTools > Utilities > Assistant (na)or runnapariafrom the command line.You can also call operations from python, e.g. as shown in thisdemo notebook.InstallationYou can installnapari-cupy-image-processingusing conda:mamba install -c conda-forge cupy cudatoolkit=11.2 napari-cupy-image-processingTroubleshooting installationIn case of issues, follow theinstructions for installing cupy.A more detailed example for installation (change 11.2 to your desired CUDA version):mamba create --name cupy_p39 python=3.9 
conda activate cupy_p39And then:mamba install -c conda-forge cupy cudatoolkit=11.2 napari-cupy-image-processingContributingContributions are very welcome. Addingcupy ndimagefunctions is quite easy as you can see in theimplementation of the current operations.
If you need another function in napari, just send a PR. Please make sure the tests pass locally before submitting a PR.pip install pytest-cov pytest-qt
pytest --cov=napari_cupy_image_processingThisnapariplugin was generated withCookiecutterusing with@napari'scookiecutter-napari-plugintemplate.LicenseDistributed under the terms of theMITlicense,
"napari-cupy-image-processing" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.