1. Overview¶
The ASTEC suite is aimed at segmenting and tracking cells from series of membrane-labeled images acquired by the multiview SPIM (MuViSPIM) light-sheet microscope. Hence, several steps should be done sequentially. Astec philosophy is to segment one image and to forward propagate the segmentation in the series while identifying cell divisions.
astec_fusion aims at fusing the 4 images per timepoint acquired by the MuViSPIM microscope.
Tuning the microscope acquisition parameters (if not known) is described in Section 5.1.
The imaged sample may move (with a large motion that can not be recovered by the registration method used here), either between the two points of view of one timepoint acquisition, or between two timepoints. astec_drift has been designed to recover these last transformations that will be used by ref:cli-fusion afterwards for fusion. Section 5.3 exemplifies this two-step fusion procedure.
astec_mars aims at segmenting one timepoint (one fused image). It is basically a seeded watershed algorithm with the regional minima as seeds. Since some segmentation errors may occur, astec_manualcorrection provides some means to perform corrections (by fusing oversegmentations, and by specifying additionnal seeds).
astec_astec aims at propagating a segmentation from one timepoint to the next, while recognizing cell divisions and building a cell lineage.
astec_postcorrection aims at doing a first (automated) round of corrections of the propagated segmentation.
astec_manualcorrection can be used as well to correct the propagated segmentation if required. Morphonet is also an alternative for that purpose.