Skip to content

[ngio] Refactor masked_loading_wrapper logic to do relabeling in the masking step #787

Open
@jluethi

Description

@jluethi

I have revisited how we handle masking & relabeling to fix #785 . For the moment, I do the relabeling in segment_ROI. In ngio, we'll want to do this in the wrapper class that handles the masking (currently masked_loading_wrapper). The main reason:

Current approach doesn't 100% guarantee consecutive labels. Within the cellpose task, there could be labels that are taken into account for relabeling but are masked away afterwards. That's very unlikely to be an issue, because we set the background to 0 in the input image. But the mock testing ignores the input

Metadata

Metadata

Assignees

No one assigned

    Labels

    Type

    No type

    Projects

    Status

    TODO

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions