Python FlowFishMaster

Flow of process:

channel image separation - noise remove (Gaussian 3x3) - nucleus channel left border shade correction - filtering on max intensity of nucleus ch
feature - cell nucleus mask - signal channel background/SN - filtering ??
image correction - blur restoration - channel pixel position adjustment - flu leakage compensation
feature
filtering
spot detection

Gating S1: Nucleus channel intensity (no nucleus / cell) [Fluid CAM] 　　　max_intensity S2: nucleus position (whole cell not / only a slice of cell in field of view) [fluid CAM] center_x border_pixels_ratio S3: nucleus mask area circularity -> Aggregation(slice cell) 　S4: signal intensity no signal-> Bright spot staining failure S5: total/mean intensity of nucleus area

Next Step Is the nuclear mask able to cover the bright spots of Ch2 / 4-> implement spot detection in python? Sure Need to save simultaneous passage?

Config & results mi_shares: config: general: (system wide config) gate: (parameters used in gating) spot: (spot detection) results: images:

Results directory structure: results: /run /imgs /res