Package: workshop-demo
workshop-demoA demo napari plugin incorporating reader, writer and dock widget contributions using the new npe2 plugin architecture.Thisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.InstallationYou can installworkshop-demoviapip:pip install workshop-demoTo install latest development version :pip install git+https://github.com/DragaDoncila/workshop-demo.gitWhat is this?This plugin was created to serve as a semi-meaningful example of a plugin using
the new naparinpe2architecture.It provides a reader, a writer and two dock widgets to support opening, processing
and writing outcell tracking challengedata.We've provided comments and example tests that can be used as a reference
when building your own plugin.Using this pluginSample DataYou can download sample data for this plugin from the tracking challenge website. Any 2D+T
sequence should work, but this plugin has been tested only with theHuman hepatocarcinoma-derived cells expressing the fusion protein YFP-TIA-1dataset.Reading DataThis plugin's reader is designed for tracking challenge segmentation gold standard ground truth
data conforming to the file format described in thedata specification.Ground truth data is only provided for a subset of the frames of the entire sequence. This
reader will attempt to find the number of frames of the associated sequence in a sister
directory of the ground truth data directory and open a labels layer with the same number
of frames, thus ensuring the labelled data is correctly overlaid onto the original sequence.https://user-images.githubusercontent.com/17995243/146114062-36124c05-f44a-488e-8991-f39a702c917f.movSegmenting DataOne of the dock widgets provided by this plugin is "Segment by Threshold". The widget
allows you to select a 2D+T image layer in the viewer (e.g. any of the sequences in the Human
hepatocarcinoma dataset above) and segment it using a selection of scikit-image thresholding functions.The segmentation is then returned as aLabelslayer into the viewer.https://user-images.githubusercontent.com/17995243/146114088-f6fb645e-8d78-4880-827b-2f0334dad859.movHighlighting Segmentation DifferencesThe second dock widget provided by this plugin allows you to visually compare your segmentation
against the ground truth data by computing the difference between the two and adding this as a
layer in the napari viewer.To use this widget, open it from the Plugins menu and select the two layers you wish to compare.https://user-images.githubusercontent.com/17995243/146114112-c891723f-8640-4708-8014-c78731fb3396.movWriting to ZipFinally, you can save your segmentation to a zip file whose internal directory structure
will closely mimic that of the tracking challenge datasets, so that it may be opened
again in the viewer.To save your layer, choose File -> Save selected layer(s) withonelabels layer selected,
then select label zipper from the dropdown choices.https://user-images.githubusercontent.com/17995243/146114163-ee886990-979c-4756-97c5-aaf2c39dccde.movContributingContributions 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,
"workshop-demo" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.