Edit temporal links Plugins

Addlink Plugin

class morphonet.plugins.EditTemporalLinks.Addlink.Addlink

Bases: MorphoPlugin

This plugin creates temporal links at several time points on objects sharing the same label. After the execution, the lineage property is updated.

This plugin requires selecting objects across different time points using labels.

Parameters:

objects – The labeled objects on MorphoNet

Delink Plugin

class morphonet.plugins.EditTemporalLinks.Delink.Delink

Bases: MorphoPlugin

This plugin delete temporal links at several time points on objects sharing the same label. After the execution, the lineage property is updated.

This plugin requires selecting objects, optionally across several time points using labels.

Parameters:

objects – The labeled objects on MorphoNet

Tracko Plugin

class morphonet.plugins.EditTemporalLinks.Tracko.Tracko

Bases: MorphoPlugin

This plugin creates a complete object lineage using the maximum of overlap between objects. The overlap is calculated between the bounding box enveloping each object. After the execution, the lineage property is updated. This plugin requires a segmentation.

Parameters:

• intensity_channel (int, default: 0) – The desired channel of the intensity images used for tracking

• downsampling (int, default: 2) – Downsampling applied to intensity images, the higher the downsampling , the faster the plugin will run, but worse the result quality

• time_direction (list) – Forward : The tracking is performed from the current time point to last one. Backward : The tracking is performed from the current time point to first one

• optical_flow (string) – none : No optical flow. TV-L1 : TV-L 1 optical flow method https://scikit-image.org/docs/0.23.x/api/skimage.registration.html#skimage.registration.optical_flow_tvl1 iLK :iterative Lucas-Kanade pptical flow method https://scikit-image.org/docs/0.23.x/api/skimage.registration.html#skimage.registration.optical_flow_ilk

• links (number of) – all : create all possible links (backward and forward mode) 2: can create 2 daughters links, in backward mode only (in forward, it creates only 1 link) 1: create only 1 links (backward and forward mode)

morphonet.plugins.EditTemporalLinks.Tracko.get_iou_bbox(bb1, bb2)

Calculate the Intersection over Union (IoU) of two bounding boxes.