Ion detection series

Bright-spot/single-ion detection and ion-state discrimination: the BrightSpots, SingleIonPresent and IonState analysis processes.

Module overview

Module	Class	Detection method	Purpose
`ion_blob`	`BrightSpots`	Threshold segmentation + connected-component counting	Counts the number of ions in each frame
`bright_spots`	`BrightSpots`	skimage `blob_dog`	Detects bright spots and outputs a position mask and bloblist
`single_ion_present`	`SingleIonPresent`	Counting + multiple Gaussian-fit-parameter criteria	Decides whether a single ion is present
`ion_state`	`IonState`	Multi-image sequences by imgindex	Discriminates the ion product state

Discrimination workflow

IonState collects the check / survival / hot / shelved image series by imgindex, detects whether an ion is present in each image, and aggregates the results into the product state:

group frames by imgindex (check / survival / hot / shelved)
        ↓ detect the ion in each frame by blob analysis
     aggregate → publish the product-state result

Usage

from quatm.analysis.ion_state import IonState

det = IonState(name="ionstate")   # subscribe to the image streams and group by imgindex
det.run()

Each process is started from the Analysis Manager (AnalysisManager), where it is selected with a checkbox; image streams, thresholds, imgindex, etc. are configured in the property tree.