Plot tracks in latent space and real space #135
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mattersoflight
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Aug 15, 2024
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@ziw-liu let's use this PR to coordinate development of the plotting features we need next.
applications/contrastive_phenotyping/contrastive_cli/plot_embeddings.py
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Co-authored-by: Ziwen Liu <[email protected]>
ziw-liu
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Aug 15, 2024
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@Soorya19Pradeep Current commit shows how to use TripletDataModule to load data from a specific track_id and render in napari.
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* animated latent space * delete duplicate umap calculation --------- Co-authored-by: Shalin Mehta <[email protected]>
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@Soorya19Pradeep Note that the animated plot will be missing legend items (e.g. infected) if the class is not present in the first frame. This is an upstream issue. |
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@Soorya19Pradeep as discussed offline, please refactor this script to generate a "report of embeddings" with a curated test set of cells annotated for cell division and infection events. Let's compare these plots (on confluence) for the model you just trained and the similar model trained with a larger FOV. |
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This PR aims to add plotting utilities to visualize features (or their dimensionally reduced versions) over tracks of single cells, alongside images of the same tracked cell.