dchaley / dchaley/deepcell-segmentation

Split compartment postprocessing into separate tasks

Open
#389 0 comments 0 reactions 0 assignees View on GitHub
Dominant language
Jupyter Notebook
Stars
9
Forks
2
PR merge metrics
No merged PRs in 30d

Description

The prediction model always generates both compartments, and puts them into a single file (2 pairs of predictions, 4 arrays total). Then, postprocessing on each is independent.

Instead of saving to a shared raw predictions file, and later to a shared predictions file, we should separate everything into the compartment. For example,

raw-predictions-whole-cell.npz
predictions-whole-cell-mask.npz
predictions-whole-cell-shapes.json

This would let computation happen in parallel, and also reduce memory requirements by ~2x pixel size.

Contributor guide

No contributing guide indexed for this repository

Assessment

This issue has not been assessed yet.

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.