Set up BioCLIP 2 app code based on BioCLIP demo

#1
HDR Imageomics Institute org
edited Jun 5

Using example images from the first BioCLIP demo, updating the code to run inference with BioCLIP 2 and uses pybioclip and select TreeOfLife-200M sample images.

Due to space persistent storage limitations, embeddings are fetched from the TreeOfLife-200M repo and metadata for the images comes from demo-data. The images will be retrieved from an S3 bucket, as with the original bioclip demo.

egrace479 changed pull request title from Add example images from BioCLIP app to Set up BioCLIP 2 app code based on BioCLIP demo
HDR Imageomics Institute org
edited Jun 5

@vimar and @thompsonmj , this should function (without returning images) once we have the embeddings merged into TreeOfLife-200M (this PR) and bioclip-2/metadata.parquet is added to the demo-data repo (using download to local folder to address persistent storage restrictions).

Image return will have to wait for the S3 bucket to be setup, but the code is in place.

HDR Imageomics Institute org

Parquet file turned out smaller than expected, so I added it too. Images are currently being uploaded, but otherwise this should be ready to go.

egrace479 changed pull request status to merged

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