embedder

Method to compute per-cell embeddings for all JUMP-CP data.

How to use this method

In the instructions below we use this method via Docstore and Terra to generate embeddings for one plate from the cpg0016-jump dataset. When tested in May 2024, this example plate took less than 1 hour to process via the workflow and cost $3.

1. Download to your local file system the file single_plate_example_inputs.json which holds input parameters for an example JUMP-CP plate.

2. Go to https://dockstore.org/workflows/github.com/jump-cellpainting/embedder and click on Launch with: Terra.

3. Either create a new Terra workspace or choose an existing workspace into which to import the workflow method. Either way, you will be automatically redirected to the Terra page for the newly imported workflow.

4. On the Terra workflow page:

   1. Select Run workflow with inputs defined by file paths.
   2. Then click on Drag or click to upload json and choose the file single_plate_example_inputs.json which you downloaded in the first step.
   3. Set the value of parameter embeddingOutputPath to be a Google Cloud Storage path of your choosing, such as a folder within your Terra Workspace bucket.
   4. Click Save
   5. Click Run Analysis

When the workflow completes, Terra will send a notification email.