Skip to content
This repository has been archived by the owner on Oct 19, 2024. It is now read-only.

Feature/h5 tile feature writer #69

Closed
wants to merge 2 commits into from

Conversation

AjeyPaiK
Copy link
Member

This PR adds the following features to ahcore:

  1. Adds H5TileFeatureWriter which can write tile features to an H5 file. (Fixes Implement a callback to store the feature vectors extracted by the foundation model. #66)
  2. Makes appropriate modifications to H5FileImageReader so that The feature vectors can be read in such a way that they can be reorganised corresponding to their original spatial coordinates.

@AjeyPaiK AjeyPaiK requested review from jonasteuwen and EricMarcus-ai and removed request for jonasteuwen February 22, 2024 14:23
@AjeyPaiK
Copy link
Member Author

AjeyPaiK commented Apr 4, 2024

This isn't necessary since the existing writer initializes a dataset with variable length. So, when writing feature vectors to the H5 file, the writer is initialised automatically with the feature dimension.

Check below:

  1. We have a feature extractor that outputs a feature vector of length 768. There are 18042 tiles in the WSI I chose to test this. The dataset initialised by the writer has the right dimensions.

image

Sign up for free to subscribe to this conversation on GitHub. Already have an account? Sign in.
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

Implement a callback to store the feature vectors extracted by the foundation model.
1 participant