cellcanvas / embedding-projector / 0.0.1

Generate a Tensorboard projector for visualzing the embeddings

Automatically generate Tensorboard event files and launch a visualizer for it. Currently suppot zarr and npy files.
Tags
imagingcryoetPython
Citation
Solution written by
Zhuowen Zhao
License of solution
MIT
Source Code

Arguments

--embeddings
Path to the feature vector embeddings (default value: PARAMETER_VALUE)
--labels
Path to the labels correspond to the embeddings. Default is None. (default value: PARAMETER_VALUE)
--embed_zarr_key
Key to get the embeding zarr file. Default is None. (default value: PARAMETER_VALUE)
--label_zarr_key
Key to get the label zarr file. Default is data. (default value: PARAMETER_VALUE)
--label_img
Path to the npy image files corresponds to the embeddings. Default is None. (default value: PARAMETER_VALUE)
--logdir
Output directory name in the current working directory/runs. Default is runs/tensorboard (default value: runs/tensorboard)
--k
Percentage of the features to visualize (<= 1000). Default is 0.01 (default value: 0.01)
--port
Port number to launch Tensorboard server. Default is 6006 (default value: 6006)

Usage instructions

Please follow this link for details on how to install and run this solution.