Closed shntnu closed 1 year ago
@Arkkienkeli A couple questions that I'm happy integrate into the documentation before merging:
collated
, consensus
, and embeddings
folders?efficientnet_v2_imagenet1k_s_feature_vector_2_ec756ff
which part of the string is an identifier for the deep learning network and which part the hash for the model?For @shntnu
.parquet
files be .parquet
or do we allow other file types? .csv.gz? .sqlite?@ErinWeisbart
collated
- contains csv or parquet files with well-level profiles for all plates.
consensus
- contains csv or parquet files with treatment-level profiles.
embeddings
- contains npz or parquet files with single-cell features (extracted from single full image).
In this example, efficientnet_v2_imagenet1k_s_feature_vector_2_ec756ff
-> efficientnet
- name of the network (EfficientNet), imagenet1k
- the dataset that was used for training, ec756ff
- hash.
We also agreed with @shntnu that it is possible to use other identifiers for model, for example zenodo doi (see folder structure for DeepProfiler).
Thanks so much Nikita. I've moved things around a little bit and added some additional information to the documentation based on your help. @Arkkienkeli and @shntnu would you take a look to make sure that what I've added is correct? Then I'm happy to have this merged.
@ErinWeisbart Looks good to me! Thank you.
@ErinWeisbart LGTM!
Thanks for the edits :)
I've moved things around a little bit and added some additional information to the documentation based on your help. @Arkkienkeli and @shntnu would you take a look to make sure that what I've added is correct? Then I'm happy to have this merged.
@ErinWeisbart @Arkkienkeli many thanks! Merging now
Related: https://github.com/jump-cellpainting/aws/issues/85#issuecomment-1245809221