Package: napari-allencell-annotator
napari-allencell-annotatorA plugin that enables image annotation/scoring and writes annotations to a .csv file.
Plugin provided by the Allen Institute for Cell Science.The Allen Cell Image Annotator plugin for napari provides an intuitive
graphical user interface to create annotation templates, annotate large
image sets using these templates, and save image annotations to a csv file.
The Allen Cell Image Annotator is a Python-based open source toolkit
developed at the Allen Institute for Cell Science for both blind, unbiased and un-blind
microscope image annotating. This toolkit supports easy image set selection
from a file finder and creation of annotation templates (text, checkbox, drop-down, and spinbox).
With napari's multi-dimensional image viewing capabilities, the plugin seamlessly allows users to
view each image and write annotations into the custom template.
Annotation templates can be written to a json file for sharing or re-using. After annotating,
the annotation template, image file list, and the annotation values
are conveniently saved to csv file, which can be re-opened for further annotating.Supports the following image types:OME-TIFFTIFFCZIPNGJPEGThisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.Installation1. PrerequisitesThe plugin requiresConda.Installing on WindowsFollow the steps linked above exceptOn step 8, check top the box to add to PATHInstalling on Mac2. Install the pluginClick the link corresponding to your OS.WindowsFrom the link above, click the three dots on the top menu bar and select download.Open a file explorer and go to the Downloads folder. UseOption 1below. A prompt window should open and start installing. If this fails useOption 2.Option 1: Double-click the fileinstall_napari.shOption 2: Search the file finder for Anaconda Prompt. Open version 3. Run the following commands one line at a time.conda create -n napari_annotator python=3.9 anacondaconda activate napari_annotatorpython -m pip install --upgrade pippython -m pip install "napari[all]"python -m pip install napari-allencell-annotatornapariStill not working?Try using conda forge instead of pip.Ex: conda install -c conda-forge napari instead of python -m pip install "napari[all]"MacOS/UnixFrom the link above, download the file.Open terminal.Runchmod +x ./Downloads/install_napari.commandIf you get a file not found error try adjusting the path to match where install_napari.command was downloaded.Open finder, navigate to the file, double-clickinstall_napari.command.A terminal window should open and start installing.3. Launch the PluginOnce the napari window opens, go toPlugins.Ifnapari-allencell-annotator: Annotatoris listed click it to launch.If it is not listedInstall/Uninstall Plugins⇨ check the box next tonapari-allencell-annotator⇨close⇨Plugins⇨napari-allencell-annotator: Annotator.4. Re-opening the Plugin After InstallingWindowsSearch for anaconda navigator in file finderClick on navigator version 3Once the navigator opens, clickEnvironmentson the left sideClick on the annotator environment and wait for it to loadPress the play buttonTypenapariin the prompt that opensClickPlugins⇨napari-allencell-annotator: AnnotatorMacOSOpen terminalRun these commands one line at a timeconda activate napari_annotatornapariClickPlugins⇨napari-allencell-annotator: AnnotatorQuick StartOpen napariStart the pluginOpen napari, go to "Plugins" ⇨ "napari-allencell-annotator".Create or import annotations and add images to annotate.For more detailed usage instructions, check out thisdocumentContributingContributions 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-allencell-annotator" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.