Use pixelflow for two realistic use-cases

alan-turing-institute / pixelflow

BSD 3-Clause "New" or "Revised" License

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Use pixelflow for two realistic use-cases #4

Open ots22 opened 1 year ago

ots22 commented 1 year ago

[x] Use case 1 (to decide - e.g. one from Evie)
[x] Use case 2 (to decide - e.g. one from Marjan)

quantumjot commented 1 year ago

btrack would be another use-case.

We have a slightly more customised version of the basic pixelflow functionality here. It'd be nice to swap this out for a fully featured version of pixelflow.

evangeline-corcoran commented 1 year ago

For use case 1 we can use the seed segmentation pipeline as it seems relatively straightforward to replicate what I have already to get seed size and shape measurements, but more efficiently

quantumjot commented 1 year ago

Here's another use case: https://github.com/lowe-lab-ucl/btrack-examples/blob/main/examples/segmented.tif

masks only, but the images are TYX, meaning that pixelflow needs to be executed separately for each T