Table 1.

Model organisms with their digital representation

Animal species	Outline	Software utilities	In toto	In vivo	References
C. elegans	Manual lineage tree extraction and comparison of different embryos.	SIMIBiocell	Yes	Yes	[124]
	Semiautomatic tracking and annotations at the single cell resolution up to 350 cells	StarryNite and AceTree	Yes	Yes	[8, 11, 97]
	Automated analysis of reporter gene expression in Caenorhabditis elegans with cellular resolution	StarryNite and AceTree	Yes	Yes	[96]
	Digital nuclear atlas of first larval stage (L1) at single-cell resolution from confocal imaging of 15 individual worms	VANO	Yes	No	[78, 108]
	Analysis of cell fate from single-cell gene expression profiles	VANO	Yes	No	[77]
	Tracking and analysis at the single cell resolution	NucleiTracker4D	Yes	Yes	[39]
C. intestinalis and H. roretzi	Quantitative reconstruction and analysis of digital data at the cellular scale	Imaris and Amira	Yes	No	[132, 133]
C. intestinalis	Interactive developmental table	–	Yes	No	[57]
	Manual segmentation of the tailbud embryo and analysis of its anatomy	Amira	Yes	No	[98]
Drosophila melanogaster	3D reconstruction and analysis of gastrulation movement	Imaris	No	Yes	[87, 131]
Zebrafish	Imaging and reconstruction of the first 24 h of development from DLSLM imaging 3D + time data	Matlab	Yes	Yes	[63]
	Imaging and reconstruction of the first 10 cleavages from multiharmonic microscopy imaging	Mov-It	Yes	Yes	[101]