Saravanan666/pypi-org huggingface dataset:
Package: napari-amdtrk
napari-amdtrkAmend segmentation and track within napari manually.:eyes: watch a demo videoInput data structureNapari-amdtrk reads an input directory which includes:An intensity image (tif) in txyc (or txy) formatAn object mask (tif) in txy formatAn object table (csv) with following essential columns:frame: time frametrackId: ID of the track, starting from 1Center_of_the_object_0: x coordinateCenter_of_the_object_1: y coordinatecontinuous_label: the corresponding label (intensity value) of the object in the object mask (You may useskimage.measure.labelto get it from a binary mask).A config file namedconfig.yaml(other names are not allowed)Within the config file, there should be:intensity_suffix: suffix of the intensity image (e.g., forfoo_GFP.tif, useGFPin the config). For multiple intensity images, separate them with commas (e.g.,GFP, mCherry)mask_suffix: suffix of the mask imagetrack_suffix: suffix of the tracked object tableframe_base: index of the first frame (either0or1)stateCol:optionalcolumn name for the cell state (e.g., cell cycle phase) in the object table. Leave blank if the object table does not contain itNapari-amdtrk will modify mask and track files in place.Other files are not affected.Quick startOpennapariGUI.File>Open folder> chooseAmend segmentation and trackPlugins>napari-amdtrk: Amend track widget>RunInlayer list, select thesegmlayer to start editing.Please check out the demo videohereand the sample data (see below).Sample dataTo load sample data,File>Open Sample>napari-amdtrk>basic tracksorcomplete cell cycle tracks.basic tracks: simple cell tracks as essential input data.complete cell cycle tracks: cell tracks with additional cell cycle features.The above operations will download data to~/.amd_trk/_sample_data/(~230MB). After downloading is finished, sample data will be loaded.NotesPlease cite this repository if using the plugin in your work (tryAbout>Cite this repositoryupper right of this homepage).Sample data (cell track videos) have been published withpcnaDeep: a fast and robust single-cell tracking method using deep-learning mediated cell cycle profiling. We acknowledge Dr Kuan Yoow Chan and members of his lab for generating the data.Keyboard shortcuts↑and↓: toggle different operationsenter: run the operationAvailable to a selected object:control+9: shrink the object maskcontrol+0: expand the object maskThisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.InstallationPlease installnapariGUI first:python -m pip install "napari[all]"You can installnapari-amdtrkviapip:pip install napari-amdtrkLicenseDistributed under the terms of theMITlicense,
"napari-amdtrk" is free and open source softwareIssuesIf you encounter any problems, please [file an issue] along with a detailed description.
Package: napari-animated-gif-io
napari-animated-gif-ioOpen and save 3D image stacks as animated gifsYou find the menus for opening and saving animated gifs in theTools > File Import/Exportmenu:Furthermore, if in 3D view, you can save the current view with a little tilt animation as animated gif.
Under the hood this uses themicrofilmlibrary.Thisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-animated-gif-ioviapip:pip install napari-animated-gif-ioTo install latest development version :pip install git+https://github.com/haesleinhuepf/napari-animated-gif-io.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-animated-gif-io" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-animation
napari-animationnapari-animationis a plugin for making animations innapari.Merlin Langeusednapari-animationto create one ofNature's best science images for September 2022This plugin is built onnaparimoviefrom @guiwitz. naparimovie was submitted to napari inPR#851before napari plugin infrastructure existed.Overviewnapari-animationprovides a framework for the creation of animations in napari, the plugin contains:an easy to use GUI for creating animations interactivelya Python package for the programmatic creation of animationsThis plugin remains under development and contributions are very welcome, please open an issue to discuss potential improvements.InstallationPyPInapari-animationis available through the Python package index and can be installed usingpip.pipinstallnapari-animationLocalYou can clone this repository and install locally withpip install -e .Interactive usenapari-animationcan be used interactively.An animation is created by capturingkeyframescontaining the current viewer state.To activate the GUI, selectnapari-animation: wizardfrom theplugins menuHeadlessnapari-animationcan also be run headless, allowing for reproducible, scripted creation of animations.fromnapari_animationimportAnimationanimation=Animation(viewer)viewer.dims.ndisplay=3viewer.camera.angles=(0.0,0.0,90.0)animation.capture_keyframe()viewer.camera.zoom=2.4animation.capture_keyframe()viewer.camera.angles=(-7.0,15.7,62.4)animation.capture_keyframe(steps=60)viewer.camera.angles=(2.0,-24.4,-36.7)animation.capture_keyframe(steps=60)viewer.reset_view()viewer.camera.angles=(0.0,0.0,90.0)animation.capture_keyframe()animation.animate('demo.mov',canvas_only=False)ExamplesExamples can be found in ourexamplesfolder. Simple examples for both interactive and headless
use of the plugin follow.ContributingContributions are very welcome and a detailed contributing guide is coming soon.Tests are run withpytest.We usepre-committo sort imports withisort, format code withblack, and lint withflake8automatically prior to each commit.
To minmize test errors when submitting pull requests, please installpre-commitin your environment as follows:pre-commitinstallLicenseDistributed under the terms of theBSD-3license,
"napari-animation" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-annotator
napari-annotatorA lightweight plugin extending label layer control.Thisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.DescriptionThis lightweight plugin helps you navigate your labels layer. It is intended to ease your manual annotation work.Select a label from the list.Toggle the visibility of individual label entries.Move to the centroid of a label at the current zoom.Change the color of individual labels.Erase all drawn pixels of a given label.Restore an erased label.UsageStart the pluginPlugins > napari-annotator: Annotator.The plugin will list available labels once a labels layer is selected and labels drawn.Color shuffling for labels will not work, since the plugin sets the color mode of the layer todirect.
But you can always change the color of individual labels, using the color picker.Known limitationsLag when drawing (probably related tothis issue).Locating / moving to the center of a label only works on 2D/3D label layers, i.e.:single- / multi-channel 2D label layers.single-channel 3D label layers (the third dimension being either Z or T).Maximum 255 labels supported. Increasing number of supported label is possible, but when increasing it, colors in the canvas will mismatch the layer control and plugin entries (probably related tothis issue)Restoring an erased labels is lost after switching between layers.InstallationYou can installnapari-annotatorviapip:pip install napari-annotatorTo install latest development version :pip install git+https://github.com/loicsauteur/napari-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 theBSD-3license,
"napari-annotator" is free and open source software.IssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Or open a thread onforum.image.scwith a detailed description
and a@loicsauteurtag.
Package: napari-apple
napari-appleDetection of apple based on YOLOv4 modelThisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.InstallationFirst, please note that this moduleonly workson a Linux Ubuntu system. Indeed, the launch of the YOLO module is a command that is executed on a Linux Ubuntu system.Before you can operate the module, you must install thenapari-applemodule and Darknet on your machine.Instruction for napari-moduleYou can installnapari-appleviapip:pip install napari-appleTo install latest development version :pip install git+https://github.com/hereariim/napari-apple.gitInstruction DarknetDarknet is the module where the pre-trained YOLO model is located. You can install Darknet by running this command:git clone https://github.com/pjreddie/darknet
cd darknet
makeWhen Darknet is installed, you have to put the weights of the apple detection model in the cfg subfolder. You find the weights in the weight-darknet folder.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-apple" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-apr-viewer
napari-apr-viewerA simple plugin to create and view APR images in napariUsageTo get started, open an image of your choice (2D or 3D grayscale) in napari and open theconvert_image_to_aprpanel. Select the image layer to convert, an appropriate data type, and hitRun.Note:choosing a data type smaller than the input type may lead to overflow and thus erroneous results.Conversion parameters can often be left to their default values, thanks to the automatic parameter tuning. For very noisy images, it is sometimes useful to increase thesmoothingparameter. In order to get a more (or less) aggressive adaptation, change therelative errorparameter.To save the result to file, simply save the newly created layer using theFilemenu. We use the extension.apr, although the file is actually written inhdf5format (and can be opened/explored as such). In this example, the APR is roughly 80 times smaller than the original image on disk. APR files can be opened directly in napari, e.g. by drag and drop.To better understand the workings of the APR on your data, you can use theAPR Viewerpanel to change theView modefor a selected APR layer tolevel. This shows you a visualization of the adaptive resolution. Particles in the brightest regions correspond exactly to pixels (lossless), while each shade darker corresponds to downsampling by a factor of 2 in each dimension.TheDownsampleslider can be used to reduce the resolution of the displayed data for the selected layer. This can be used to explore large volumes in 3D, where rendering the full data requires too much memory.Note:We do not offer APR-native rendering at this time, so this step will reconstruct the entire pixel volume (at the selected resolution). Thus, for large volumes, be sure to increase the downsampling before toggling the 3D viewer.The data shown in these examples was taken from the Platynereis-ISH-Nuclei-CBG dataset availablehere.Thisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-apr-viewerviapip:pip install napari-apr-viewerContributingContributions 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-apr-viewer" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-arboretum
Arboretumhttps://github.com/lowe-lab-ucl/arboretum/assets/8217795/d98c22c4-73bb-493a-9f8f-c224d615209dAutomated cell tracking and lineage tree reconstruction.OverviewA dockable widget forNaparifor visualizing cell lineage trees.Features:Lineage tree plot widgetIntegration withbtrackUsageOnce installed, Arboretum will be visible in thePlugins > Add Dock Widget > napari-arboretummenu in napari. To visualize a lineage tree, (double) click on one of the tracks in a napariTrackslayer.ExamplesYou can use the example script to display some sample tracking data in napari and load the arboretum tree viewer:python./examples/show_sample_data.pyAlternatively, you can usebtrackto generate tracks from your image data. See the example notebook here:https://github.com/quantumjot/btrack/blob/main/examplesHistoryThis project has changed considerably. TheTrackslayer, originally developed for this plugin, is now an official layer type in napari. Read the napari documentation here:https://napari.org/stable/api/napari.layers.Tracks.htmlTo view the legacy version of this plugin, visit the legacy branch:https://github.com/quantumjot/arboretum/tree/v1-legacy
Package: napari-argos-archive-reader
napari-argos-archive-readerA plugin to read Dioptic ARGOS archive filesThis repo contains a reader plugin forDIOPTIC ARGOSArchive files, which
have.zipfile extension.
Individual ARGOS layers are grouped into napari layer with stacks according to
their illumination, stage XY position and Z-stack information.The plugin implements delayed reading usingdask.delayedso that one can quickly
see the contents even for large archives with many layers. Note!: switching to
volume rendering or swapping axes can trigger the loading of all ARGOS layers, which
can take a long time for large archives.ARGOSis an automated system
for surface inspection according to ISO 10110-7.This plugin is still experimental and does not support all features of ARGOS archives.Currently, the plugincan read Argos matrix archives containing regular image layers including:✅ segmentation masks✅ Z-stack metadata✅ Illumination metadata✅ proper scaling and affine transformation of layerscan read ❔✅ Argos line scan (polar) archives with minimal support (no metadata parsing)
This has not been tested on many archives.Not supported are:❌ annotated archives❌ pyramid image structures❌ Line segmentation metadata❌ color metadata❌ ...UsageOpening filesSimply drag and drop an ARGOS Archive.zipfile onto the napari canvas or useFile->Opento open it.Synchronizing contrast limitsBy default, after reading an archive, each napari layer will have their own contrast limits, so you can
adjust these contrast limits individually.The reader plugin registers a custom key binding after reading an ARGOS archive. Pressing theskey will allow
you to synchronize the contrast limits for a set of layers:If you selecta singlenapari layer corresponding to an image/stack from an ARGOS archive, all napari image
layers that were loaded from this archive now have their contrast limits synchronized, i.e. changing the
contrast limits ofanyof them will adjust the contrast limits ofallof the layers belonging to the same
archive.If you selectmultiplenapari layers and presssall of these and only these napari layers will have
their contrast limits synchronized, regardless of whether they belong to the same ARGOS archive or not.InstallationIf you have napari installed you can install the plugin from the napari hub through thePlugins -> Plugin Mangermenu
entry. After waiting a short while for napari to retrieve the plugins available from the hub, simply enter "argos" in
the filter line entry field at the top to narrow down the plugin list and click install.You can installnapari-argos-archive-readerviapip:pip install napari-argos-archive-readerTo install latest development version :pip install git+https://github.com/dioptic/napari-argos-archive-reader.gitLicenseDistributed under the terms of theMITlicense,
"napari-argos-archive-reader" is free and open source software
Package: napari-arnheim
Napari - ArnheimIdeaNapari Arnheim bundles Napari with the Arnheim Framework Client and its Grunnlag-ProviderPrerequisitesNapari Arnheim only works with a running Arnheim Instance (in your network or locally for debugging) and a Grunnlag-Provider. (see Grunnlag)UsageIn order to initialize the Client you need to connect it as a Valid Application with your Arnheim Instancebergen=Bergen(host="HOST_NAME",port=8000,client_id="APPLICATION_ID_FROM_ARNHEIM",client_secret="APPLICATION_SECRET_FROM_ARNHEIM",name="karl",)withnapari.gui_qt():viewer=napari.Viewer()viewer.window.add_dock_widget(ArnheimWidget(bergen=bergen),area="right")Testing and DocumentationSo far Bergen does only provide limitedunit-tests and is in desperate need of documentation,
please beware that you are using an Alpha-VersionBuild withArnheimBergenGrunnlagNapariRoadmapThis is considered pre-Alpha so pretty much everything is still on the roadmapDeploymentContact the Developer before you plan to deploy this App, it is NOT ready for public releaseVersioningThere is not yet a working versioning profile in place, consider non-stable for every releaseAuthors**Johannes Roos ** -Initial work-jhnnsrsSee also the list ofcontributorswho participated in this project.LicenseAttribution-NonCommercial 3.0 Unported (CC BY-NC 3.0)AcknowledgmentsEVERY single open-source project this library used (the list is too extensive so far)
Package: napari-bacseg
napari-BacSegBacterial segmentation and analysis platform than can inport/export files in multiple formats. Integrating many tools such as Cellpose, ColiCoords, Oufti/MicrobeTracker.Thisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.Installing BacSegCreate a virtual environment and then activate it:conda create –-name napari-bacseg python==3.9
conda activate napari-bacsegInstallnapari-bacsegviapip:pip install napari-bacsegLaunch Napari:NapariSelectnapari-bacsegfrom thePluginsdropdown menuInstalling BacSeg From GitHubconda create –-name napari-bacseg python==3.9
conda activate napari-bacseg
conda install -c anaconda git
conda update --all

pip install napari[all]

pip install git+https://github.com/piedrro/napari-bacseg.gitUpdating BacSeg From GithubOnce you have installed the plugin, you can update the plugin by running the following commands:pip install git+https://github.com/piedrro/napari-bacseg.gitGPU InstallationOnce you have installed the plugin, you can install the GPU version of the plugin by running the following commands:pip uninstall torch
conda install pytorch torchvision torchaudio pytorch-cuda=11.7 -c pytorch -c nvidiaIf the latest CUDA versions don't work, try an older version like cuda 11.3:pip uninstall torch
conda install pytorch torchvision torchaudio cudatoolkit=11.3 -c pytorch -c nvidiaContributingContributions 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-bacseg" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-basicpy
napari-basicpyBaSiCPy illumination correction for napariExample:Thisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-basicpyviapip:pip install napari-basicpyTo install latest development version :pip install git+https://github.com/tdmorello/napari-basicpy.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-basicpy" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-bbox
napari-bboxA new layer for bounding boxes in 2+ dimensionsNote: This plugin was originally part ofAnnotation Toolbox, and was separated to allow other plugins to utilize it.Demohttps://user-images.githubusercontent.com/36735863/227506511-d672ce5c-eab5-436f-a7fd-6080e118a9a8.mp4Thisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-bboxviapip:pip install napari-bboxTo install latest development version :pip install git+https://github.com/bauerdavid/napari-bbox.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-bbox" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-bee-annotator
napari-bee-annotatorDeveloped by theEPFL Center for Imagingfor theMobile Robotic Systems Groupin Dec 2023.
This napari plugin provides an easy way for the researches to annotate honey bees leaving/entering the hive. The annotations will serve as ground truth for the validation of various automated animal tracking approaches.InstallationYou can installnapari-bee-annotatorviapip:pip install napari-bee-annotatorTo install latest development version :pip install git+https://github.com/EPFL-Center-for-Imaging/napari-bee-annotator.gitGetting startedOpen napari with the plugin and your video using the following commandnapari -w napari-bee-annotator --plugin video path/to/video.mp4. Note that you need to havenapari_videoinstalled to readmp4files.Select the orientation of your video: horizontal/vertical refers to the direction of the bee's leaving/entering the hive.Start annotating: A simple left click indicates a bee moving up or to the left depending on the orientation selected. You can hold down the shift key to annotate a bee moving down or to the right. Annotations can be deleted with a right click on the annotation you want to delete. To move to the next frame, you can either hold downctrland scroll with the mouse wheel or click on the play button. Playback parameters, such as the playback speed, can be changed by right clicking on the play button.Saving and loading tracks: To save a tracks layer selected from the list of layers and click onFile > Save selected layers. Choose a name and the csv extension. If you want to continue to work on the annotations for a specific video, you first have to load the corresponding csv file by clicking onOpen with Plugin > Open file(s).... Select the file you want to load and click on open. A dialog should pop up that asks you to select the reader to use for loading the csv file. SelectBee annotator. Lastly, you have to tell the plugin to interact with the layer you just loaded by selecting it in theTracks layerdrop down menu.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-bee-annotator" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: napari-bfio
napari-bfioA plugin to read and write images using bfio within napariThisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.InstallationYou can installnapari-bfioviapip:pip install napari-bfionapari-bfiodepends onbfiopackage to read/write the data. By default,bfiopackage and the core dependencies (numpy, tifffile, imagecodecs, scyjava) are installed during the installation process ofnapari-bfio.To install latest development version :pip install git+https://github.com/PolusAI/napari-bfio.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-bfio" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.