search

SydneyBioX / simpleSeg

https://sydneybiox.github.io/simpleSeg/
1 stars 0 forks source link

Optimise parameters #4

Open ellispatrick opened 2 years ago

ellispatrick commented 2 years ago

1) Run simpleSeg on multiple CODEX + IMC datasets to see if there is a set of parameters that work well on all of them.

2) Research metrics that could be used to optimise segmentation using a grid search. eg, signal to noise, roundness of nuclei....

ellispatrick commented 2 years ago

Predicting the segmentation mask with the marker that was used to predict it could be useful. This would allow us to extract a prediction probability and use this for the watershed, this might be more "standardised".

ellispatrick commented 1 month ago

Did Shila develop a package that could help with this?