Plant phenotyping example

[kasra-hosseini]

Summary

These todos were collected while testing the notebooks on plant images.

TODO

• [ ] Work with images stored in non-flat file directories
  • [ ] e.g., we can create unique IDs from the path: plantID_data_filename
• [ ] In annotation, we assume that all parent images are stored in one directory. Can we make this a bit more flexible, e.g., "/path/to/*/*.png"?
• [ ] Count the number of pixels in parent images (x and y), add as metadata
• [ ] Add a warning/error when the number of pixels in x or y directions are different from what we expect.
• [ ] Colorbars, transparency for out of the range patches?
• [x] normalize_mean and normalize_std in 003_train_classifier need to be set based on the plant images.
  • [ ] Refer: https://github.com/Living-with-machines/MapReader/issues/31
• [ ] Data augmentation and transformations for the plant images, e.g., the intensities or brightness, mimic the changes in light/brightness.
• [x] Multiple views, compare different side-views, they should be the same scale (for each side view), transfer learning
• [ ] Change over time, which features emerge first
• [x] Chain of classifiers? The first classifier would decide plant/no and then classify the flower/greenspace, then the shape of the features. Classify green features into different groups.
  • [ ] Refer: https://github.com/Living-with-machines/MapReader/issues/32
• [x] torchvision and MapReader installation issue

[kasra-hosseini]

Chain of classifiers? The first classifier would decide plant/no and then classify the flower/greenspace, then the shape of the features. Classify green features into different groups.

• The first classifier has three labels : None / Flower / Leaf. The second classifier will be designed later.

Also refer to: https://github.com/Living-with-machines/MapReader/issues/32

[kasra-hosseini]

Multiple views, compare different side-views, they should be the same scale (for each side view), transfer learning

• WIP, we have two sets of labelled data. One for top view and the other for side views. Training has been done only on the top view.

[kasra-hosseini]

normalize_mean and normalize_std in 003_train_classifier need to be set based on the plant images.

Refer to: https://github.com/Living-with-machines/MapReader/issues/31

[dcsw2]

Hi @evangeline-corcoran is this ticket live? We are just doing some spring-cleaning of this board and would like to close it if possible? Do you need the contents somewhere else? If so can you move it?

[evangeline-corcoran]

Hi @dcsw2 I've moved the relevant info elsewhere, so you can go ahead and close this.