Hey #teamtomo, if you often find yourself using the excellent membrain-seg from @lorenzlamm.bsky.social et al., you might find my napari plugin "napari-segselect" useful. Let's say your tomogram contains the edges of two bacterial cells, each with a membrane and cell wall: - ThreadSky

About ThreadSky

Hey #teamtomo, if you often find yourself using the excellent membrain-seg from @lorenzlamm.bsky.social et al., you might find my napari plugin "napari-segselect" useful. Let's say your tomogram contains the edges of two bacterial cells, each with a membrane and cell wall:

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lorenzlamm.bsky.social•22 days ago

That looks super useful for selecting membranes and cleaning up noise!! Looking forward to trying :)

bwmr.bsky.social•22 days ago

If you want to split them up into individual segmentations, to assign different colors, or create masks for further processing, etc., membrain-seg has the flag "--store-connected-components", which assigns each connected volume a unique ID.

bwmr.bsky.social•22 days ago

"napari-segselect" automatically opens the "*_segmented.mrc" files from membrain-seg as a label field...

bwmr.bsky.social•22 days ago

... and allows you to easily create labels containing only the IDs of interest.

bwmr.bsky.social•22 days ago

... which can then be written out as binary masks in the mrc format and visualized or used however you like:

bwmr.bsky.social•22 days ago

You can find the plugin on napari-hub here: https://www.napari-hub.org/plugins/napari-segselect
and the GitHub repository here: https://github.com/bwmr/napari-segselect

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