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[FEATURE] Output cell probability from CLI #1023

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cam-nowell opened this issue Oct 7, 2024 · 0 comments
Open

[FEATURE] Output cell probability from CLI #1023

cam-nowell opened this issue Oct 7, 2024 · 0 comments
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enhancement New feature or request

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@cam-nowell
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Is your feature request related to a problem? Please describe.
We are running a custom (from scratch) trained model of nome neurons using the Fiji wrapper. The output masks get a little wonky if the neurites link up and form loops. Using the cellprobabilty output and doing our own extraction seems to work well. But we can't get cell proabbility output from the Fiji wapper as there isn't a CLI command for it. But we cna get them out one at a time from the GUI

Describe the solution you'd like
A CLI flag that allows the saving out or generation of the cell proability images

Describe alternatives you've considered
Manually doing each image thorugh the GUI, not ideal fro 100s of images

.

@cam-nowell cam-nowell added the enhancement New feature or request label Oct 7, 2024
@cam-nowell cam-nowell changed the title [FEATURE] [FEATURE] Output cell probability from CLI Oct 15, 2024
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