cytomining/DeepProfiler-handbook

Improvements to profiling chapter - Issue on page /docs/07-profiling.html

Opened this issue · 5 comments

jccaicedo commented
  • This chapter should come before training!
  • The order of profiling options should be:
    • The Cell Painting CNN first
    • ImageNet pre-trained second
    • Your own trained model third

Also, is it true that we strongly recommend to prepare the dataset (compression) before profiling? I thought DeepProfiler was able to compute features for images without compression (which is desirable if the dataset is too large). Our model is robust to illumination changes, so this should not affect downstream performance. I recommend to remove this and instead clarify that DeepProfiler does not need compression to profile (I added a Note with this comment in Chapter 3).

Arkkienkeli commented
  • Reordered chapters (swap training and profiling)
  • Reordered profiling sections
  • Removed recommendation about data pre-procsessing from profiling section ; I kept it in training only as we discussed yesterday.
  • 👍2
Arkkienkeli commented

Cell Painting CNN: expects pre-defined order of Cell Painting channels.

Arkkienkeli commented

Cell Painting CNN: expects pre-defined order of Cell Painting channels.

Added this information.

Arkkienkeli commented

Added links to notebooks and the code.

jccaicedo commented

I could not find the links to notebooks or code. Was this part of this page?

In any case, it'd be great to link to the following resources, just to make the page navigation friendly:

  • Links to config files for each profiling option.
  • Links to the config file section that talks about profiling options.

If you add this, you can close this issue @Arkkienkeli