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## Data Meeting Update (Feb. 17, 2023)
### Cell Type Controls Clean-up
* Icon buttons with tooltips to save space
* Channel chips colored with channel color if that channel is opened
![](https://i.imgur.com/eth6IPX.png)
### Imported Embedding Visualization and Training
* Embeddings can be loaded, currently from embeddings.json in a zip file which is parsed into an array
* Sample image and embedding data
    * File-name: `/nb/data-registry/data/labels/static/2d/Tissue-Lymph_Node/Liu_Validation_MIBI/Slide27Stain5_Point11_R1C10.npz:`
    * Distribution: `total: 2354
    cell_types:
      BCELL: 1472
      ENDOTHELIAL: 78
      TCELL: 746
      MACROPHAGE: 58`
    * Julie's embeddings from: `np.savez_compressed("/workspace/output/embeddings.npz", embedding=embedding, y_truth=y_truth, file_names=file_names, cell_indices=cell_indices)`

Cell Types | UMAP | Raw Image
:---:|:---:|:---:
![](https://i.imgur.com/g126WQB.png) | ![](https://i.imgur.com/zGeOUEh.png) | ![](https://i.imgur.com/gsYy5xN.png)


* Embeddings can also be trained on with hand-labeled data

Parameters | Loss Curve (confusion matrix has issues right now)
:---:|:---:
![](https://i.imgur.com/1114opV.png) | ![](https://i.imgur.com/2Vthzpi.png)

"Hand-labeled" | Prediction From Embedding | Ground Truth
:---:|:---:|:---:
![](https://i.imgur.com/wP5XvGl.jpg) | ![](https://i.imgur.com/o2UtTQ1.png) | ![](https://i.imgur.com/gsYy5xN.png)

* As we can see, cells with thrown out cell types need to either be removed from segmentation or labeled OTHER
### Other concerns, some more things to tackle
* Tried weighting classes proportionally by number of samples (tensorflow.js does not have built in imbalanced loss metrics) and results were much worse
* Streamlined data loading (including npz support) and export