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bauerdavid / napari-nD-annotator

BSD 3-Clause "New" or "Revised" License
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Create documentation for the plugin #23

Open bauerdavid opened 2 years ago

bauerdavid commented 2 years ago

Started creating the documentation for the plugin using Sphinx. It will be available on readthedocs.org.

GenevieveBuckley commented 2 years ago

Thanks for this, more documentation is definitely needed. This is what I came up with after converting the README gif to mp4, then stepping through the frames one by one.

  1. Install the plugin into a new conda environment
conda create -n test-ndannotator python=3.9 pip ipython
conda activate test-ndannotator
conda install napari
python -m pip install napari-nD-annotator

  1. Open example data with ipython

    import napari
from skimage.data import cells3d
import numpy as np
viewer = napari.Viewer()
nuclei = cells3d()[:, 1]
viewer.add_image(nuclei, colormap="magma")
viewer.add_labels(np.zeros_like(nuclei))

  2. Create some bounding boxes Plugins > napari-nd-annotator > Object list

In the Object List widget, click the button "Create Bounding box layer" Draw some bounding boxes

  1. Annotate an object In the Object List widget, click one one of the objects now in the list. A new widget will appear with orthoslice views of the object - don't click on it, you can ignore it for now. In the main napari canvas, draw around the object. This is editing the new "Cropped Labels" layer, created by the plugin. Do this for several slices

  2. Interpolate ??? I'm not sure which widget is the one we are supposed to use here. They both seem to interpolate between the slices, but the gif in the README seems to look a bit more like an older version of the Annotation Tollbox widget...

Plugins > napari-nd-annotator > Annotation toolbox or Plugins > napari-nd-annotator > Slice interpolation

Check which dimension to interpolate along. Click "Interpolate"

GenevieveBuckley commented 2 years ago

I'm still not sure about the difference between the "Annotation toolbox" and "Slice interpolation" widgets. The layouts look almost identical, so I'm not sure how the function differs.

I also think maybe the widget in the README gif is outdated? None of the widgets I can open have the same layout & number of buttons.

bauerdavid commented 2 years ago

Thanks for your work! Actually the Interpolation Widget is included in the Annotation Widget. When we finally get there, the Annotation Widget will have three different tools in separate tabs, and one of them will be the Interpolation Widget. Also the autofill objects option appears above the tab view. Maybe not exposing the Interpolation Widget as a separate plugin would be less confusing. You are right, unfortunately the gif was not updated to show the current state of the plugin... I will update it as soon as I get there.