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spacetx / starfish

starfish: unified pipelines for image-based transcriptomics
https://spacetx-starfish.readthedocs.io/en/latest/
MIT License
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Tutorials making use of Napari should include screenshots of expected output. #1925

Closed vals closed 3 years ago

vals commented 3 years ago

[ Related to openjournals/joss-reviews#2440 ]

The tutorials should include screenshots of the expected Napari window when this feature is demonstrated. E.g. https://spacetx-starfish.readthedocs.io/en/latest/gallery/quick_start/plot_quick_start.html#sphx-glr-gallery-quick-start-plot-quick-start-py or https://spacetx-starfish.readthedocs.io/en/latest/gallery/pipelines/3d_smFISH.html#load-data-run-pipeline-display-results or the bottom section of https://spacetx-starfish.readthedocs.io/en/latest/gallery/how_to/plot_display.html

For https://spacetx-starfish.readthedocs.io/en/latest/gallery/how_to/plot_display.html in particular, it would be good to annotate the screenshots with e.g. arrows pointing to the ‘stack [1]’ layer. Similar should also be done in other potential tutorials demonstrating building on the interactive visualization.

neuromusic commented 3 years ago

As noted in the discussion on openjournals/joss-reviews#2440, we've strived to make our documentation fully-automated. However, incorporating napari into the documentation building as resulted in failures on ReadTheDocs that we weren't able to debug.

I have removed references to the interactive display utility from the example pipelines in #1938 and will replace the interactive visualizations in the Quick Start with matplotlib-based visualizations.