mehta-lab / microDL

3D virtual staining with 2D and 2.5D U-Nets
BSD 3-Clause "New" or "Revised" License
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Metadata Structure #203

Closed Christianfoley closed 1 year ago

Christianfoley commented 1 year ago

Current metadata structure needs to be reworked to create robust of state preservation of the dataset:

  1. Image statistics (normalization, flatfields, etc) should be stored directly with the data
  2. Training and inference hyperparameters (namely: config hyperparameters, data splits, inference metadata) should be stored with the configs
  3. Tensorboard logs from training and inference should be stored with the model. This means a refactoring and combining of the model directory naming scheme for training, and the logdir naming scheme for inference. (related mehta-lab/viscy#19)
Christianfoley commented 1 year ago

Good feature request from @Soorya19Pradeep related to this:

I think this general idea of having the model 'look for' channels can also extend to the other metadata computed at training time.

Christianfoley commented 1 year ago

Implemented restructuring of metadata storage in commit 2bbfc62