diff --git a/src/aliby/baby_sitter.py b/src/aliby/baby_sitter.py index 064b3748f432d147e627da4954b6c03c07ae389b..386e312b3d06edc13916829fabc6a24618dd6d9f 100644 --- a/src/aliby/baby_sitter.py +++ b/src/aliby/baby_sitter.py @@ -15,24 +15,30 @@ class BabyParameters(ParametersABC): def __init__( self, modelset_name, + pixel_size, clogging_thresh, min_bud_tps, isbud_thresh, + session, ): """Initialise parameters for BABY.""" self.modelset_name = modelset_name + self.pixel_size = pixel_size self.clogging_thresh = clogging_thresh self.min_bud_tps = min_bud_tps self.isbud_thresh = isbud_thresh + self.session = session @classmethod def default(cls, **kwargs): """Define default parameters; kwargs choose BABY model set.""" return cls( modelset_name=get_modelset_name_from_params(**kwargs), + pixel_size=0.182, clogging_thresh=0.75, min_bud_tps=3, isbud_thresh=0.5, + session=None, ) def update_baby_modelset(self, path: t.Union[str, Path, t.Dict[str, str]]): @@ -78,9 +84,11 @@ class BabyRunner(StepABC): else: brain = modelsets.get( modelset_name, + pixel_size=parameters.pixel_size, clogging_thresh=parameters.clogging_thresh, min_bud_tps=parameters.min_bud_tps, isbud_thresh=parameters.isbud_thresh, + session=parameters.session, ) self.crawler = BabyCrawler(brain) self.brightfield_channel = self.tiler.ref_channel_index