Tutorial Updates & other July 20, 2023 Hack-a-thon Day Tasks

[HaleySchuhl]

To Do list

Check off an issue once the Pull Request is merged in. To assign yourself to an issue, edit this section and add your name beside the issue. Also assign yourself in the issue which is linked. Once you open a PR, add a tag to it as well.

• [x] Documentation updates for max_value removal, really just within_frame.md since tutorials will be updated significantly and separately #1194
• [x] Missing documentation page tabulate_bayes #1227 --> #1318
• [x] Deprecate get_nir #1232 --> @HaleySchuhl #1294
• [x] Deprecate hyperspectral.analyze_spectral #945 --> @HaleySchuhl #1295

Tutorial Updates

VIS

• [x] https://plantcv.readthedocs.io/en/latest/tutorials/vis_tutorial/ --> done by @kmurphy61 and ready for review
• [x] https://github.com/danforthcenter/plantcv-tutorial-v4-VIS-single-plant
• [x] PR: #1303

  Thermal

• [x] https://plantcv.readthedocs.io/en/latest/tutorials/thermal_tutorial/ --> @lacostag & Haley finishing
• [x] https://github.com/danforthcenter/plantcv-tutorial-thermal
• [x] PR: #1302

  VIS-NIR

• [x] https://plantcv.readthedocs.io/en/latest/tutorials/vis_nir_tutorial/ --> @leowlima & Haley finishing up
• [x] https://github.com/danforthcenter/plantcv-tutorial-vis-nir
• [x] PR: #1301

  Grayscale

• [x] https://plantcv.readthedocs.io/en/latest/tutorials/nir_tutorial/ NIR tutorial (rename/rebrand as a grayscale tutorial) --> @HaleySchuhl
• [x] https://github.com/danforthcenter/plantcv-tutorial-grayscale
• [x] PR: #1300

  Photosynthesis

• [x] https://plantcv.readthedocs.io/en/latest/tutorials/psII_tutorial/ --> @kmurphy61 in progress, may wait until psII is updated for final version
• [x] https://github.com/danforthcenter/plantcv-tutorial-photosynthesis
• [x] PR: #1336

  Hyperspectral

• [x] https://plantcv.readthedocs.io/en/latest/tutorials/hyperspectral_tutorial/ --> @maliagehan
• [x] https://github.com/danforthcenter/plantcv-tutorial-hyperspectral
• [x] PR: #1313

  Machine learning

• [x] https://plantcv.readthedocs.io/en/latest/tutorials/machine_learning_tutorial/ --> @HaleySchuhl
• [x] github.com/danforthcenter/plantcv-tutorial-machine-learning
• [x] #1306

  Multi-plant

• [x] https://plantcv.readthedocs.io/en/latest/tutorials/multi-plant_tutorial/ this one is highly outdated, we have deprecated a handful of the multi-plant analysis methods that have been improved upon. Evaluate if this tutorial is still helpful. --> done by @kmurphy61 and ready for review
• [x] https://github.com/danforthcenter/plantcv-tutorial-v4-multiobject
• [x] PR: #1305

  Seeds

• [x] https://plantcv.readthedocs.io/en/latest/tutorials/seed_analysis_tutorial/ --> @Stylopidae1793
• [x] https://github.com/danforthcenter/plantcv-tutorial-seeds
• [x] PR: #1316

  Morphology

• [x] https://plantcv.readthedocs.io/en/latest/tutorials/morphology_tutorial/ : this one has a more detailed tutorial using sorghum here and they are so similar that it might be better to combine and then credit all 3 contributors. @joshqsumner
• [x] https://github.com/danforthcenter/plantcv-tutorial-morphology
• [x] PR: #1308

  Color correction

• [x] https://plantcv.readthedocs.io/en/latest/tutorials/transform_color_correction_tutorial/ --> @nfahlgren
• [x] https://github.com/danforthcenter/plantcv-tutorial-color-correction --> @HaleySchuhl
• [ ] PR: https://github.com/danforthcenter/plantcv/pull/1339 #1339

  Input/Output

• [x] https://plantcv.readthedocs.io/en/latest/tutorials/input_output_tutorial/ : believe this one is significantly outdated but the goal is to show off various ways to read in different types of image data and ways to save out data. This "methods of saving out data" is actually a recent topic of discussion and involved append vs overwriting behaviors in CSV vs JSON. --> @joshqsumner
• [x] https://github.com/danforthcenter/plantcv-tutorial-input-output
• [x] PR: #1311

  Thresholding

• [ ] https://plantcv.readthedocs.io/en/latest/tutorials/threshold_tutorial/ --> @zeeuqsze
• [ ] https://github.com/danforthcenter/plantcv-tutorial-threshold
• [ ] PR:

  ROIs

• [x] https://plantcv.readthedocs.io/en/latest/tutorials/roi_tutorial/ --> use the multi-plant tutorial by @kmurphy61 as a template, uses point-and-click ROIs, grid ROIs, need to add other shapes, partial vs. cutto to a roi_tutorial
• [x] https://github.com/danforthcenter/plantcv-tutorial-roi --> @HaleySchuhl
• [ ] PR: #1339

Watershed

• [x] https://plantcv.readthedocs.io/en/latest/tutorials/watershed_segmentation_tutorial/ --> @maliagehan
• [x] https://github.com/danforthcenter/plantcv-tutorial-watershed
• [x] PR: #1298

Exist in v3 and need updating

• [x] Arabidopsis Multi-Plant Workflow (template?) ¶ - https://github.com/danforthcenter/plantcv/pull/1338
  • [x] still has max_value in threshold function, could this be our first "template"?
  • [x] yea still has pcv.find_objects so needs updating to v4 totally
• [ ] HOMOLOGY https://plantcv.readthedocs.io/en/release-4.0/tutorials/homology_tutorial/
  • [x] tutorial 1
  • [x] tutorial 2
  • [x] tutorial 3
  • [x] tutorial 4
  • [ ] docs update https://github.com/danforthcenter/plantcv/pull/1339

Don't live in the tutorial gallery yet and need to be added (after v4 release)

• [ ] https://github.com/danforthcenter/plantcv-tutorial-segment-image-series
• [ ] https://github.com/danforthcenter/plantcv-interactive-tutorials
• [ ] https://github.com/danforthcenter/plantcv-tutorial_leaf_instance_segmentation

User tutorials

• [x] https://github.com/danforthcenter/plantcv-homology-tutorials
• [ ] Rice chalkiness
• [ ] https://github.com/danforthcenter/plantcv-tasselyzer-tutorial
• [ ] https://github.com/danforthcenter/plantcv-tutorial-interactive-pollent-count
• [ ] https://github.com/danforthcenter/plantcv-stomata-tutorial @kmurphy61 will update to be v4

[HaleySchuhl]

@kmurphy61 we just merged the changes to PSII that rename light and dark frames. Just say the word and I can update the Photosynthesis tutorial if you'd like, but I'm working under the assumption you'd want to update them 🥇

[nfahlgren]

I updated the notebook locally today to make the workshop notebook, so I can push those changes later

[HaleySchuhl]

@zeeuqsze what's the status with your tutorial updates? Would you like for me to carry that one to the finish line or should we temporarily remove that tutorial until we can become clear on the difference between tutorials, templates, and lesson plans? haha