Implement a tomogram segmentation as part of pixelflow.

alan-turing-institute / pixelflow

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Implement a tomogram segmentation as part of pixelflow. #56

Open crangelsmith opened 7 months ago

crangelsmith commented 7 months ago

We would like to use pixel flow as part of the CAKED data loader. The functionality has already been implemented as part of the affinityvae project, details in here:

https://github.com/alan-turing-institute/affinity-vae/blob/develop/tools/create_subtomo.py

Inputs:

Full tomogram
Coordinates of detections with labels (the labels are optional)

Out:

PixelflowResult (with nested numpy arrays for each subtomogram), with labels indexed if provided.

crangelsmith commented 7 months ago

I think this should be not only for tomograms but could work with 2D data as well!